I carried out a system scan last night and my Avast software found 2 viruses at blk00128.dat and 00129.dat. I had read about someone putting bits of a virus into the blockchain once, is that what that is?
Most likely. People have figured out how to encode the data for a virus in the blockchain but that cannot do anything since the virus is not executed. However, you need to make sure that your antivirus doesn't delete any files in that folder (and the bitcoin data directory in general) otherwise that will cause you to need to resync.