I'd suggest running your hdd manufacturers diagnostic program, could be a hdd issue causing the problem.
If your unable to identify your hdd manufacturer use either Seagate Seatools which has a generic test which will work on any drive or download EMSA Diskcheck
If either show any errors, back up your data and try running chkdsk. If this fails to correct any errors you can either try doing a zero format (you may need to do several passes) and full reinstall or try this program HDD Regenerator
. If either of these fail then it will be a new hdd.
The ultimate BootCD
has several tools which will perform a zero wipe of the disk, it even has all the hdd manufacturers testing tools so if you have boardband this is the best option.
If these don't show any errors then I'd suggest posting a hijackthis log in this section of the forum
for someone to check that you are not infected.