Also having this issue. When my pc close it exits all applications (RR etc) and then I get a message waiting to close mapmonkey.exe. I have to click "End Now" for the computer to shutdown properly.
I have found a workaround for those who are interested:
In the registry - HKU\.Default\Control Panel\Desktop
set the following values-
AutoEndTasks = 1
WaitToKillApp = 500 (5sec Default 2000=20sec)
This will exit all non responsive programs when you shutdown.