If the icons exist in the dock then they must be still running in Mac OS X. Do you see them in the Activity Monitor?
The Task Manager in Windows doesn't show the apps still running in Windows?
There must be a strange bug that lets Parallels know that you have started an app but not when you've ended an app...
I turned on "Use detailed log messages" in Parallels Desktop Preferences. Then tried running and quitting NotePad multiple times and looking at the log messages in the parallels.log file using Console.app.
When you run a program, you should get the following for each occurrence of the program you're running (I got this while using Windows XP and Parallels Desktop 5.0.9370):
Code:
D SGAC /gui:3190:207/ Helper bundle "/Users/joevt/Documents/Parallels/BootCamp2.pvm/Windows Applications/Notepad [1].app" versionStatus=0: helperVmUuid="{9f710d3c-a320-49f5-af00-4efa3e9980b2}", currentVmUuid="{9f710d3c-a320-49f5-af00-4efa3e9980b2}", helperVersion="6.5", currentVersion="6.5"
Then you get the following for each occurrence of the program that you quit since the last time you started an occurrence of the program. I think psn is a Carbon ProcessSerialNumber. They should have just used PID...
Code:
I SGAC /gui:3190:207/ Helper with psn={0, 2454103} not running anymore
Then this (where 10443 is a PID for the help app):
Code:
I SGAC /gui:3190:207/ Found registered Vm with name="BootCamp2" for vmUuid="{9f710d3c-a320-49f5-af00-4efa3e9980b2}" (vmWrap=0x4425d00)
I SGA_ /SCTool:10443:903/ Vm uuid in reply is ok
Then a repeat of the "not running anymore" messages. Then another helper bundle message. Then this:
Code:
I SGAC /gui:3190:207/ Running helper with psn={0, 2519655} attached to launched guest application
And finally another helper bundle message.
When you quit an occurrence of the program, you should get:
Code:
D SGAC /gui:3190:207/ HELPER_USELESS(psn={0, 2519655}), line=3375
I SGAC /gui:3190:207/ No use in running helper with psn={0, 2519655}, i=12, bundlePath="/Users/joevt/Documents/Parallels/BootCamp2.pvm/Windows Applications/Notepad [1].app"
I SGAC /gui:3190:207/ Failed to find helper for guest app with appGUID={0xf90, 0x0, 0x0, 0x0} and appPath="C:\WINDOWS\system32\notepad.exe"