there are also two programs i find useful when trying to track down what is running on your computer: filemon and regmon.
they will show what is running and when. I like to start a program while having both of those programs running so i can see where in the registry it is looking, and what other files it is calling. its a long shot for you, but it might help you figure out what is happening.
both are available here:
http://www.sysinternals.com/ntw2k/source/filemon.shtml