i seriously doubt that you have a virus in your mobo. Like soul said, make sure that the virus is completely gone. You can download free programs (like ccleaner and Spybot Search & Destroy) or i can hook you up with Eset's Nod32.
Another route that you might have to think about is what the virus did to your OS. A lot of viri, when infecting your comp, will replace/remove files, leaving you with corrupt install. Unless you can restore those files, you might be looking at a re-install.
Btw, flashing ur CMOS is not a setting in your BIOS. It's a jumper on your mobo
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