Okay, here is what happened when I tried to restore the HKCU...\Run entry back. It restored it to the wrong location in HKCU.
Here is the HCKU\Software\Wow6432 key BEFORE the restore.
Windows Registry Editor Version 5.00
"Version"="8,0,6001,18762"
"Locale"="*"
"Version"="8,0,6001,18702"
"Locale"="*"
"Version"="1,1,1,9"
"Locale"="EN"
"Version"="6,0,6001,18000"
"Locale"="*"
"Username"="Tom"
"Version"="11,0,6000,6324"
"Locale"="EN"
"Version"="6,0,6001,18167"
"Locale"="en"
"Version"="8,0,6001,18762"
"Locale"="en"
And here is what PT 2009 Restore did to this key.
Windows Registry Editor Version 5.00
"Version"="8,0,6001,18762"
"Locale"="*"
"Version"="8,0,6001,18702"
"Locale"="*"
"Version"="1,1,1,9"
"Locale"="EN"
"Version"="6,0,6001,18000"
"Locale"="*"
"Username"="Tom"
"Version"="11,0,6000,6324"
"Locale"="EN"
"Version"="6,0,6001,18167"
"Locale"="en"
"Version"="8,0,6001,18762"
"Locale"="en"
"WeatherWatcherLive"="\"C:\\Program Files (x86)\\Weather Watcher Live\\ww.exe\""