Yeap, same here. I'm suspecting something messed up in a Avast update, because it happened after an update.
So, in my case, Windows XP Professional, copmputer witha a floppy disk drive. After startup rootkit warning appeared, and istead try to ask uncle Google what the hell is happening, I've chosen delete, and scan. Well, computer is still scanning right now (I'm writing from my second one, Windows XP HE (both are SP3), but without floppy drive , and no warning so far. Both of them are running Avast, latest version, free).
So, if you guys are writing, that warning reapears after rebooting, I will just ignore it.
Avast had a similar problem months ago (the reason why I have eastablished an account here), suddenly everything got marked as a virsu, because of faulty update.