Just a wild guess but it sounds like you may not have the proper directory set for FS9. Those parameters should be set first, and tested before identifying any programs that need to be shut down.
FSAutoStart uses *.ini files which you can find under the Documents and Settings folder off your root directory. Look under the Application Data folder for the FSAutoStart folder, and there should be a profile folder where the files are kept. You can print these out or edit them directly in Notepad.
--WH