You can have a HDD problem and Scan Disk checks ok..

D/L PC-Check from eurosoft (don't have the link to hand you know how to use Google..don't you) , This d/l creates a self booting floppy, boot the sick machine from this floppy..
navigate your way to the HDD tests .. the two you are interested in are the Drive mechanics, and the non destructive read, you could run the write test as well.. but I am sure that a drive mechanics test run 5 to 10 times will most likly yeild a result... if not do the read test..then a write test.. the last two will take several hours each (well used to)..

You must have a good reason to suspect a virus (btw.. I only read 33% of what you wrote..so I hope I'm not too off track)..
Have you been playing with certain types of software for you to think virus? if not and your friends are not into giveing out virii for fun..
or visiting Warez or crackz sites?
And If you have any half updated AV you should be clear of the type of virii you suspect..

cheers