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Something has corrupted my FAT.

I removed rapidblaster and other programs from my computer only to have something corrupt my FAT. I have a 40G hard drive partitioned c/d yet when fdisk is used on c, it stops at 37 or 73% and then restarts the process, running through it twice. When attempting to reinstall Windows, dll's go missing and programs hang. Have I still got a resident hidden program rewriting itself and reinfecting my hard drive? If so, how would I know? What else could be causing this problem? Would repartioning the whole drive cure this? Would low-level formatting cure this and is it possible on new drives?
I would delete the partition using DELPART or similar tool. Create a new partition and perform a full format of FAT. Run an anti-virus scanner against it. Then re-install or re-build your environment on the drive. Most viruses won't survive partition destruction, and a scanner should detect those in the MBR.

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