whels, check your task manager the next time that happens, sometimes it's a "legitimate" background processing kicking off. check to make sure windows update is turned off, or at least set to a date and time that isn't while you might be gaming. anti-virus, flash player, itunes, quicktime, java, just to name a few automatically update in the background unless you specifically turn that option off in the programs, and they can minimize a game if they kick off and take cpu priority.
iTunes, Java, AV.. all these will show activity when the tabbing is done. Whels should be able to spot which process is grabbing screen attention quite easy. Since he didn't see any obvious cause for this it must mean that either his system is messed up and a background process is interfering with his other processes unintended or he has a malicious hidden software that the scans he performed failed to detect (no tool finds all exploits).
His best bet is to disable all unnecessary startup crap from msconfig autostart programs and see if the problem continues. Nothing really NEEDS to start automatically upon startup, I would temporarily disable any software firewalls and antiviruses too. Next step would be to disable any non-ms processes from services.msc and a third step would be a total reinstall because if the previous won't work his system is hosed. Either a malware or registry corruption.
If malware is suspected, the latest rootkits cannot be reliably removed without clearing up boot sector / disk format. Otherwise he can try to reinstall over the old windows without doing format which should save a lot of trouble. Would only need to reinstall a few badly made programs that rely on registry to work.
