diff --git a/docs/source/plugins/timer.rst b/docs/source/plugins/timer.rst
index 9576f0acc20..578dd2beb50 100644
--- a/docs/source/plugins/timer.rst
+++ b/docs/source/plugins/timer.rst
@@ -1,7 +1,7 @@
 .. _plugins-timer:
 
-Timer Plugin
-============
+Game Play Timer Plugin
+======================
 
 The timer plugin records the total time spent emulating each combination of a
 system and a software list item, as well as the number of times each combination
@@ -9,12 +9,12 @@ has been launched.  To see the statistics, bring up the main menu (press **Tab**
 during emulation by default), choose **Plugin Options**, and then choose
 **Timer**.
 
-Note that this plugin records wall clock time, not emulated time.  That is, it
-records the real time duration elapsed while the emulation is running, according
-to the host OS.  This may be shorter than the elapsed emulated time if you turn
-off throttling or use MAME’s “fast forward” feature, or it may be longer than
-the elapsed emulated time if you pause the emulation of if the emulation is too
-demanding to run at full speed.
+This plugin records wall clock time (the real time duration elapsed while
+emulation is running, according to the host OS) as well as emulated time.  The
+elapsed wall clock time may be shorter than the elapsed emulated time if you
+turn off throttling or use MAME’s “fast forward” feature, or it may be longer
+than the elapsed emulated time if you pause the emulation of if the emulation is
+too demanding to run at full speed.
 
 The statistics are stored in the file **timer.db** in the **timer** folder
 inside your plugin data folder (see the
diff --git a/plugins/autofire/autofire_save.lua b/plugins/autofire/autofire_save.lua
index 1ebe06561e1..5ca4cd217b6 100644
--- a/plugins/autofire/autofire_save.lua
+++ b/plugins/autofire/autofire_save.lua
@@ -1,7 +1,7 @@
 local lib = {}
 
 local function get_settings_path()
-	return emu.subst_env(manager.machine.options.entries.homepath:value():match('([^;]+)')) .. '/autofire/'
+	return emu.subst_env(manager.machine.options.entries.homepath:value():match('([^;]+)')) .. '/autofire'
 end
 
 local function get_settings_filename()
@@ -52,7 +52,7 @@ end
 function lib:load_settings()
 	local buttons = {}
 	local json = require('json')
-	local filename = get_settings_path() .. get_settings_filename()
+	local filename = get_settings_path() .. '/' .. get_settings_filename()
 	local file = io.open(filename, 'r')
 	if not file then
 		return buttons
@@ -81,14 +81,14 @@ function lib:save_settings(buttons)
 		emu.print_error(string.format('Error saving autofire settings: "%s" is not a directory', path))
 		return
 	end
+	local filename = path .. '/' .. get_settings_filename()
 	if #buttons == 0 then
-		os.remove(path .. get_settings_filename())
+		os.remove(filename)
 		return
 	end
 	local json = require('json')
 	local settings = serialize_settings(buttons)
 	local data = json.stringify(settings, {indent = true})
-	local filename = path .. get_settings_filename()
 	local file = io.open(filename, 'w')
 	if not file then
 		emu.print_error(string.format('Error saving autofire settings: error opening file "%s" for writing', filename))
diff --git a/plugins/hiscore/init.lua b/plugins/hiscore/init.lua
index 4101dd48708..652061c92cf 100644
--- a/plugins/hiscore/init.lua
+++ b/plugins/hiscore/init.lua
@@ -23,7 +23,7 @@ end
 function hiscore.startplugin()
 
 	local function get_data_path()
-		return emu.subst_env(manager.machine.options.entries.homepath:value():match('([^;]+)')) .. '/hiscore/'
+		return emu.subst_env(manager.machine.options.entries.homepath:value():match('([^;]+)')) .. '/hiscore'
 	end
 
 	-- configuration
@@ -35,7 +35,7 @@ function hiscore.startplugin()
 		if config_read then
 			return true
 		end
-		local filename = get_data_path() .. 'plugin.cfg'
+		local filename = get_data_path() .. '/plugin.cfg'
 		local file = io.open(filename, 'r')
 		if file then
 			local json = require('json')
@@ -67,7 +67,7 @@ function hiscore.startplugin()
 		end
 		local settings = { only_save_at_exit = not timed_save }
 		-- TODO: other settings?
-		local filename = path .. 'plugin.cfg'
+		local filename = path .. '/plugin.cfg'
 		local json = require('json')
 		local data = json.stringify(settings, { indent = true })
 		local file = io.open(filename, 'w')
@@ -210,9 +210,9 @@ function hiscore.startplugin()
 	  local r;
 	  if emu.softname() ~= "" then
 		local soft = emu.softname():match("([^:]*)$")
-		r = get_data_path() .. emu.romname() .. "_" .. soft .. ".hi";
+		r = get_data_path() .. '/' .. emu.romname() .. "_" .. soft .. ".hi";
 	  else
-		r = get_data_path() .. emu.romname() .. ".hi";
+		r = get_data_path() .. '/' .. emu.romname() .. ".hi";
 	  end
 	  return r;
 	end
@@ -223,7 +223,7 @@ function hiscore.startplugin()
 	  local output = io.open(get_file_name(), "wb");
 	  if not output then
 		-- attempt to create the directory, and try again
-		lfs.mkdir( get_data_path() );
+		lfs.mkdir(get_data_path());
 		output = io.open(get_file_name(), "wb");
 	  end
 	  emu.print_verbose("hiscore: write_scores output")
diff --git a/plugins/inputmacro/inputmacro_persist.lua b/plugins/inputmacro/inputmacro_persist.lua
index 4e043852c51..6c2aa6fd188 100644
--- a/plugins/inputmacro/inputmacro_persist.lua
+++ b/plugins/inputmacro/inputmacro_persist.lua
@@ -5,7 +5,7 @@
 -- Helpers
 
 local function settings_path()
-	return emu.subst_env(manager.machine.options.entries.homepath:value():match('([^;]+)')) .. '/inputmacro/'
+	return emu.subst_env(manager.machine.options.entries.homepath:value():match('([^;]+)')) .. '/inputmacro'
 end
 
 local function settings_filename()
@@ -101,7 +101,7 @@ end
 local lib = { }
 
 function lib:load_settings()
-	filename = settings_path() .. settings_filename()
+	filename = settings_path() .. '/' .. settings_filename()
 	local file = io.open(filename, 'r')
 	if not file then
 		return { }
@@ -133,7 +133,7 @@ function lib:save_settings(macros)
 		emu.print_error(string.format('Error saving input macros: "%s" is not a directory', path))
 		return
 	end
-	filename = path .. settings_filename()
+	filename = path .. '/' .. settings_filename()
 
 	if #macros == 0 then
 		os.remove(filename)
diff --git a/plugins/timecode/init.lua b/plugins/timecode/init.lua
index 084d3b3e8d6..09e49229cae 100644
--- a/plugins/timecode/init.lua
+++ b/plugins/timecode/init.lua
@@ -34,7 +34,7 @@ function timecode.startplugin()
 
 
 	local function get_settings_path()
-		return emu.subst_env(manager.machine.options.entries.homepath:value():match('([^;]+)')) .. '/timecode/'
+		return emu.subst_env(manager.machine.options.entries.homepath:value():match('([^;]+)')) .. '/timecode'
 	end
 
 
@@ -50,7 +50,7 @@ function timecode.startplugin()
 		set_default_hotkey()
 
 		-- try to open configuration file
-		local cfgname = get_settings_path() .. 'plugin.cfg'
+		local cfgname = get_settings_path() .. '/plugin.cfg'
 		local cfgfile = io.open(cfgname, 'r')
 		if not cfgfile then
 			return -- probably harmless, configuration just doesn't exist yet
@@ -97,7 +97,7 @@ function timecode.startplugin()
 			settings.hotkey = hotkey_cfg
 		end
 		local data = json.stringify(settings, { indent = true })
-		local cfgname = path .. 'plugin.cfg'
+		local cfgname = path .. '/plugin.cfg'
 		local cfgfile = io.open(cfgname, 'w')
 		if not cfgfile then
 			emu.print_error(string.format('Error saving timecode recorder settings: error opening file "%s" for writing', cfgname))
diff --git a/plugins/timer/init.lua b/plugins/timer/init.lua
index 19755f7a348..d39243da730 100644
--- a/plugins/timer/init.lua
+++ b/plugins/timer/init.lua
@@ -1,111 +1,73 @@
 -- license:BSD-3-Clause
--- copyright-holders:Carl
-require('lfs')
-local sqlite3 = require('lsqlite3')
-local exports = {}
-exports.name = "timer"
-exports.version = "0.0.2"
-exports.description = "Game play timer"
-exports.license = "BSD-3-Clause"
-exports.author = { name = "Carl" }
+-- copyright-holders:Vas Crabb
+local exports = {
+	name = 'timer',
+	version = '0.0.3',
+	description = 'Game play timer',
+	license = 'BSD-3-Clause',
+	author = { name = 'Vas Crabb' } }
 
 local timer = exports
 
 function timer.startplugin()
-	local dir = emu.subst_env(manager.options.entries.homepath:value())
-	local timer_db = dir .. "/timer/timer.db"
-	local timer_started = false
 	local total_time = 0
 	local start_time = 0
 	local play_count = 0
+	local emu_total = emu.attotime()
 
-	local function save()
-		total_time = total_time + (os.time() - start_time)
+	local reference = 0
+	local lastupdate
 
-		local db = assert(sqlite3.open(timer_db))
-
-		local insert_stmt = assert( db:prepare("INSERT OR IGNORE INTO timer VALUES (?, ?, 0, 0)") )
-		insert_stmt:bind_values(emu.romname(), emu.softname())
-		insert_stmt:step()
-		insert_stmt:reset()
-
-		local update_stmt = assert( db:prepare("UPDATE timer SET total_time=?, play_count=? WHERE driver=? AND software=?") )
-		update_stmt:bind_values(total_time, play_count,emu.romname(), emu.softname())
-		update_stmt:step()
-		update_stmt:reset()
-
-		assert(db:close() == sqlite3.OK)
-	end
-
-
-	emu.register_start(function()
-		local file
-		if timer_started then
-			save()
-		end
-		timer_started = true
-		lfs.mkdir(dir .. '/timer')
-		local db = assert(sqlite3.open(timer_db))
-		local found=false
-		db:exec([[select * from sqlite_master where name='timer';]], function(...) found=true return 0 end)
-		if not found then
-			db:exec[[  CREATE TABLE timer (
-						driver      VARCHAR(32) PRIMARY KEY,
-						software    VARCHAR(40),
-						total_time  INTEGER NOT NULL,
-						play_count  INTEGER NOT NULL
-					  ); ]]
-		end
-
-		local stmt, row
-		stmt = db:prepare("SELECT total_time, play_count FROM timer WHERE driver = ? AND software = ?")
-		stmt:bind_values(emu.romname(), emu.softname())
-		if (stmt:step() == sqlite3.ROW) then
-			row = stmt:get_named_values()
-			play_count = row.play_count
-			total_time = row.total_time
-		else
-			play_count = 0
-			total_time = 0
-		end
-
-		assert(db:close() == sqlite3.OK)
-
-		start_time = os.time()
-		play_count = play_count + 1
-	end)
-
-	emu.register_stop(function()
-		timer_started = false
-		save()
-		total_time = 0
-		play_count = 0
-	end)
 
 	local function sectohms(time)
-		local hrs = math.floor(time / 3600)
-		local min = math.floor((time % 3600) / 60)
+		local hrs = time // 3600
+		local min = (time % 3600) // 60
 		local sec = time % 60
-		return string.format(_p("plugin-timer", "%03d:%02d:%02d"), hrs, min, sec)
+		return string.format(_p('plugin-timer', '%03d:%02d:%02d'), hrs, min, sec)
 	end
 
-	local lastupdate
-
 	local function menu_populate()
 		lastupdate = os.time()
-		local time = lastupdate - start_time
+		local refname = (reference == 0) and _p('plugin-timer', 'Wall clock') or _p('plugin-timer', 'Emulated time')
+		local time = (reference == 0) and (lastupdate - start_time) or manager.machine.time.seconds
+		local total = (reference == 0) and (total_time + time) or (manager.machine.time + emu_total).seconds
 		return
-			{{ _p("plugin-timer", "Current time"), sectohms(time), "off" },
-			 { _p("plugin-timer", "Total time"), sectohms(total_time + time), "off" },
-			 { _p("plugin-timer", "Play Count"), play_count, "off" }},
+			{
+				{ _p("plugin-timer", "Reference"), refname, (reference == 0) and 'r' or 'l' },
+				{ '---', '', '' },
+				{ _p("plugin-timer", "Current time"), sectohms(time), "off" },
+				{ _p("plugin-timer", "Total time"), sectohms(total), "off" },
+				{ _p("plugin-timer", "Play Count"), play_count, "off" } },
 			nil,
 			"idle"
 	end
 
 	local function menu_callback(index, event)
+		if (index == 1) and ((event == 'left') or (event == 'right') or (event == 'select')) then
+			reference = reference ~ 1
+			return true
+		end
 		return os.time() > lastupdate
 	end
 
+
+	emu.register_start(
+		function()
+			if emu.romname() ~= '___empty' then
+				start_time = os.time()
+				local persister = require('timer/timer_persist')
+				total_time, play_count, emu_total = persister:start_session()
+			end
+		end)
+
+	emu.register_stop(
+		function()
+			if emu.romname() ~= '___empty' then
+				local persister = require('timer/timer_persist')
+				persister:update_totals(start_time)
+			end
+		end)
+
 	emu.register_menu(menu_callback, menu_populate, _p("plugin-timer", "Timer"))
 end
 
diff --git a/plugins/timer/plugin.json b/plugins/timer/plugin.json
index 005a0fad9a4..6755f434f94 100644
--- a/plugins/timer/plugin.json
+++ b/plugins/timer/plugin.json
@@ -1,10 +1,10 @@
 {
-  "plugin": {
-	"name": "timer",
-	"description": "Timer plugin",
-	"version": "0.0.1",
-	"author": "Carl",
-	"type": "plugin",
-	"start": "false"
-  }
+	"plugin": {
+		"name": "timer",
+		"description": "Game play timer",
+		"version": "0.0.3",
+		"author": "Vas Crabb",
+		"type": "plugin",
+		"start": "false"
+	}
 }
diff --git a/plugins/timer/timer_persist.lua b/plugins/timer/timer_persist.lua
new file mode 100644
index 00000000000..5ed33f03eb4
--- /dev/null
+++ b/plugins/timer/timer_persist.lua
@@ -0,0 +1,249 @@
+-- license:BSD-3-Clause
+-- copyright-holders:Vas Crabb
+
+local sqlite3 = require('lsqlite3')
+
+
+local function check_schema(db)
+	local create_statement =
+		[[CREATE TABLE timer (
+			driver      VARCHAR(32) NOT NULL,
+			softlist    VARCHAR(24) NOT NULL DEFAULT '',
+			software    VARCHAR(16) NOT NULL DEFAULT '',
+			total_time  INTEGER NOT NULL DEFAULT 0,
+			play_count  INTEGER NOT NULL DEFAULT 0,
+			emu_sec     INTEGER NOT NULL DEFAULT 0,
+			emu_nsec    INTEGER NOT NULL DEFAULT 0,
+			PRIMARY KEY (driver, softlist, software));]]
+
+	-- create table if it doesn't exist yet
+	local table_found = false
+	db:exec(
+		[[SELECT * FROM sqlite_master WHERE type = 'table' AND name='timer';]],
+		function()
+			table_found = true
+		end)
+	if not table_found then
+		emu.print_verbose('Creating timer database table')
+		db:exec(create_statement)
+		return
+	end
+
+	-- check recently added columns
+	local have_softlist = false
+	local have_emu_sec = false
+	local have_emu_nsec = false
+	db:exec(
+		[[PRAGMA table_info(timer);]],
+		function(udata, n, vals, cols)
+			for i, name in ipairs(cols) do
+				if name == 'name' then
+					if vals[i] == 'softlist' then
+						have_softlist = true
+					elseif vals[i] == 'emu_sec' then
+						have_emu_sec = true
+					elseif vals[i] == 'emu_nsec' then
+						have_emu_nsec = true
+					end
+					return 0
+				end
+			end
+			return 0
+		end)
+	if not have_softlist then
+		emu.print_verbose('Adding softlist column to timer database')
+		db:exec([[ALTER TABLE timer ADD COLUMN softlist VARCHAR(24) NOT NULL DEFAULT '';]])
+		local to_split = { }
+		db:exec(
+			[[SELECT DISTINCT software FROM timer WHERE software LIKE '%:%';]],
+			function(udata, n, vals)
+				table.insert(to_split, vals[1])
+				return 0
+			end)
+		if #to_split > 0 then
+			local update = db:prepare([[UPDATE timer SET softlist = ?, software = ? WHERE software = ?;]])
+			for i, softname in ipairs(to_split) do
+				local x, y = softname:find(':')
+				local softlist = softname:sub(1, x - 1)
+				local software = softname:sub(y + 1)
+				update:bind_values(softlist, software, softname)
+				update:step()
+				update:reset()
+			end
+		end
+	end
+	if not have_emu_sec then
+		emu.print_verbose('Adding emu_sec column to timer database')
+		db:exec([[ALTER TABLE timer ADD COLUMN emu_sec INTEGER NOT NULL DEFAULT 0;]])
+	end
+	if not have_emu_nsec then
+		emu.print_verbose('Adding emu_nsec column to timer database')
+		db:exec([[ALTER TABLE timer ADD COLUMN emu_nsec INTEGER NOT NULL DEFAULT 0;]])
+	end
+
+	-- check the required columns are in the primary key
+	local index_name
+	db:exec(
+		[[SELECT name FROM sqlite_master WHERE type = 'index' AND tbl_name = 'timer';]],
+		function(udata, n, vals)
+			index_name = vals[1]
+		end)
+	local index_good
+	if index_name then
+		local driver_indexed = false
+		local softlist_indexed = false
+		local software_indexed = false
+		db:exec(
+			string.format([[PRAGMA index_info('%s');]], index_name), -- can't use prepared statement for PRAGMA
+			function(udata, n, vals, cols)
+				for i, name in ipairs(cols) do
+					if name == 'name' then
+						if vals[i] == 'driver' then
+							driver_indexed = true
+						elseif vals[i] == 'softlist' then
+							softlist_indexed = true 
+						elseif vals[i] == 'software' then
+							software_indexed = true
+						end
+						return 0
+					end
+				end
+				return 0
+			end)
+		index_good = driver_indexed and softlist_indexed and software_indexed
+	end
+
+	-- if the required columns are not indexed, migrate to a new table with desired primary key
+	if not index_good then
+		emu.print_verbose('Re-indexing timer database table')
+		db:exec([[DROP TABLE IF EXISTS timer_old;]])
+		db:exec([[ALTER TABLE timer RENAME TO timer_old;]])
+		db:exec(create_statement)
+		db:exec(
+			[[INSERT
+				INTO timer (driver, softlist, software, total_time, play_count, emu_sec, emu_nsec)
+				SELECT driver, softlist, software, total_time, play_count, emu_sec, emu_nsec FROM timer_old;]])
+		db:exec([[DROP TABLE timer_old;]])
+	end
+end
+
+
+local function open_database()
+	-- make sure settings directory exists
+	local dir = emu.subst_env(manager.machine.options.entries.homepath:value():match('([^;]+)')) .. '/timer'
+	local attr = lfs.attributes(dir)
+	if not attr then
+		lfs.mkdir(dir)
+	elseif attr.mode ~= 'directory' then
+		emu.print_error(string.format('Error opening timer database: "%s" is not a directory', dir))
+		return nil
+	end
+
+	-- open database
+	local filename = dir .. '/timer.db'
+	local db = sqlite3.open(filename)
+	if not db then
+		emu.print_error(string.format('Error opening timer database file "%s"', filename))
+		return nil
+	end
+
+	-- make sure schema is up-to-date
+	check_schema(db)
+	return db
+end
+
+
+local function get_software()
+	local softname = emu.softname()
+	local i, j = softname:find(':')
+	if i then
+		return softname:sub(1, i - 1), softname:sub(j + 1)
+	else
+		-- FIXME: need a way to get the implicit software list when no colon in the option value
+		return '', softname
+	end
+end
+
+
+local function get_current(db)
+	local statement = db:prepare(
+		[[SELECT
+			total_time, play_count, emu_sec, emu_nsec
+			FROM timer
+			WHERE driver = ? AND softlist = ? AND software = ?;]])
+	statement:bind_values(emu.romname(), get_software())
+	local result
+	if statement:step() == sqlite3.ROW then
+		result = statement:get_named_values()
+	end
+	statement:reset()
+	return result
+end
+
+
+local lib = { }
+
+function lib:start_session()
+	-- open database
+	local db = open_database()
+	if not db then
+		return 0, 0, emu.attotime()
+	end
+
+	-- get existing values
+	local row = get_current(db)
+	local update
+	if row then
+		update = db:prepare(
+			[[UPDATE timer
+				SET play_count = play_count + 1
+				WHERE driver = ? AND softlist = ? AND software = ?;]])
+	else
+		row = { total_time = 0, play_count = 0, emu_sec = 0, emu_nsec = 0 }
+		update = db:prepare(
+			[[INSERT
+				INTO timer (driver, softlist, software, total_time, play_count, emu_sec, emu_nsec)
+				VALUES (?, ?, ?, 0, 1, 0, 0);]])
+	end
+	update:bind_values(emu.romname(), get_software())
+	update:step()
+	update:reset()
+	return row.total_time, row.play_count + 1, emu.attotime.from_seconds(row.emu_sec) + emu.attotime.from_nsec(row.emu_nsec)
+end
+
+function lib:update_totals(start)
+	-- open database
+	local db = open_database()
+	if not db then
+		return
+	end
+
+	-- get existing values
+	local row = get_current(db)
+	if not row then
+		row = { total_time = 0, play_count = 1, emu_sec = 0, emu_nsec = 0 }
+	end
+
+	-- calculate new totals
+	local emu_total = emu.attotime.from_seconds(row.emu_sec) + emu.attotime.from_nsec(row.emu_nsec) + manager.machine.time
+	row.total_time = os.time() - start + row.total_time
+	row.emu_sec = emu_total.seconds
+	row.emu_nsec = emu_total.nsec
+
+	-- update database
+	local update = db:prepare(
+		[[INSERT OR REPLACE
+			INTO timer (driver, softlist, software, total_time, play_count, emu_sec, emu_nsec)
+			VALUES (?, ?, ?, ?, ?, ?, ?);]])
+	local softlist, software = get_software()
+	update:bind_values(emu.romname(), softlist, software, row.total_time, row.play_count, row.emu_sec, row.emu_nsec)
+	update:step()
+	update:reset()
+
+	-- close database
+	if db:close() ~= sqlite3.OK then
+		emu.print_error('Error closing timer database')
+	end
+end
+
+return lib