Your Anti Virus software is trying to tell you something .....
You have a Virus ...
Virus' , are written to do all manner of things. Some of then sit resident in memory and then infects any .exe / .com file on the drive when it is loaded into memory. It spreads throughout for drive and then onwards. This is how some / lots virus' spread.
There is no such thing as a 100% safe antivirus software. To limit the risk, you must ensure that the virus detection tables are bang up todate and kept up todate by its auto updating feature. This still doesn't garrentee that your machine is safe. Some virus checker installations become "compramised", so they will let some resident stuff get through.
Corrupt files don't flag as virus'
What I suggest.
Unistall your anti virus, and reinstall it, This will catch most situations (although it depends how old and what make your AV software is), Secondly ,Go to you AV's website and download there boot scanning application for a better chance.
After you have cleared the virus, then you have to clean up the damage, SHIII seems to be one, but there will probably be others too. But don't fix SHIII and ignore the cause, because it'll come and bite you again.
Steve
good luck,