You may be the victim of "Scareware". This is a particular sort of malware that is deliberately contrived by people who are peddling their own "anti- virus" software. The scareware attaches somehow and keeps sending panic messages that your system is infested -- using a screen that vaguely resembles the warning system that's already part of Windows or some other anti-virus program -- and it repeats itself practically everytime you click the mouse. It offers a chance to do a scan -- which, I think, actually embeds even more scareware into your system -- at the end of which it reports that dozens or hundreds of viruses and trojans made it past your existing defenses ... and now would you like to buy this guy's anti-virus program? About the only virus that program is sure to eliminate is that very scareware he infected your system with.
Usually a conventional anti-virus/trojan program (and there are several good ones on the internet available free) can stop the scareware, but these guys seem to spend more time working up scareware that will beat the protection programs than on improving the protection program that they're selling with this scareware. There are some freeware solutions to scareware (About.com has a page on it). I used one and it completely eliminated my scareware ... but it also made my desktop themes vanish until I used a restoration program
On the other hand, it could be a glitch that somehow spontaneously appears in an otherwise perfectly good anti-malware program on your machine. There was a time when one of my anti-malware programs (I use a number of them because, frankly, no single program can get all the malware) kept giving me alerts whenever I clicked a page of a favorite - and thoroughly healthy - website. Repeated scans with that and the other anti-malware programs came up with nothing, but I still got the warnings from that one program ("Anti-Vir") on every page of that one website. Finally I simply deleted the Anti-Vir program altogether and then reloaded it completely fresh (it's freeware and pretty good) and no more problems. Evidently somehow a glitch had developed in the old Anti-Vir program on my PC which was eliminated when I reloaded it using entirely new downloaded files.