Ok Guys,
Firstly I have not tested this (yet), but these values may be usefull!
Change the timeout for a prompt to kill a service\task
After recieving a shutdown request vista waits for a notification that persistant services have stopped. You can alter the wait time for Windows to kill the persistent services.
HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control
WaitToKillServiceTimeout , default value is 20000
When this value is exceeded a prompt appears to force the service\task to stop or continue to wait.
Alter the time for user process's and applications to be killed
This is the timeout before starting to shut down and kill open applications and user processes when the user want to shutdown, restart or log off.
Navigate to the following registry branch:
HKEY_CURRENT_USER\Control Panel\Desktop
WaitToKillAppTimeout, default 20000.
When the WaitToKillAppTimeout value is breached, the End Task dialog box appears, stating that the process did not respond, and allowing user to End the task.
HungAppTimeout, default 5000 - HungAppTimeout specifies how long the system waits for user processes to end after the user clicks the End Task command button in Task Manager or after the user has selected to restart or shutdown the system.
Automatically end\kill process's without a user prompt
When the values above are breached, a end task or other prompt is still generated. By changing to the value of registry key AutoEndTasks to 1, we can ask Windows to end all processes that timeout when shut down or log out from Windows automatically, without asking for user input or interaction. Default value of the key is 0, which mean no user processes will end automatically.
AutoEndTasks is located at HKEY_CURRENT_USER\Control Panel\Desktop registry branch.
I would imagine that sensable settings on the above, combines with AutoEndTasks should fix your issue ? As these are reg keys they can of course all be manipulated via group policy.