heuristics - if that option is not on in nod32 i would tick that option and all the other options that are in the control panel and do a full system scan just to be on the safe side, also i would get spybot search and destroy (if you havent already) and run that, windows defender isnt the best app in the world. I would also suggest hijackthis.
If all those show clean, then like madmatt said it could be a service or program that isnt quite ready for vista and is crashing, giving you that pop up box, i have had some strange issues on a test system after updating it from windows update