Sorry I don't mean to derail the Firefox VS. IE debate but the OP made one comment that was a lot more worrisome to me then that he was using IE (and I ride on the firefox bandwagon).

For some reason the resident scan was not on
This is what a large number of viruses and worms do, they shut down your AV scans. It is possible that you have been infected for longer then you think and through that infection your AV stuff was disabled and likely being prevented from updating. It is also possible that this is where the two viruses you did find came from.

I would clean like crazy at this point if I was you.