I use AVG myself and I've had similar virus warnings with keygens and patches/cracks in the past. But as they weren't official patches from the software company itself it's possible there could of been sneaky trojans in there as they said, so I went with AVG's advice.
But so far it hasn't caused any problems with programs I know and trust, as has happened to you.
The only other FREE anti-virus proggy that I know of (and gets highly rated by most people) is
AVAST (version 4 at the mo I think).
Comes in various flavours including of course a Home Edition that is FREE. (Windows/Linux).
Haven't tried it myself yet, but have heard good things about it. You can test drive it and let me know, then I might switch, hehe.
GET IT FROM HERE