Is there an option in your BIOS to reset to factory defaults? Have you tried that if its there? You could always try flashing it as you mentioned - seems like you have little to loose. There must be a way of wiping and reinstating the BIOS.
Have you tried another MOBO? If you suspect a faulty component, its often cheaper and faster to replace it and see if that fixes your prob. Just replace one thing at a time till you're back in business.
Also booting off a CD or floppy may not get you around a BIOS virus, as BIOS needs to boot first in order to even be able to see any drives attached.