Long ago and far away, I came across a similar posted problem. No matter if they let the drive do a full scan or not, it would still run chkdsk every boot. It came down to something described as the "dirty bit" function. Windows has a bit that it turns on, and I think it stored it in an odd spot in the boot sector, saying that it thinks the hard drive is making or has made bad sectors, run chkdsk (or scandisk in 98/me). In win2k/XP (more so XP) this can get "stuck" and does not go away no matter how many scans you do. The answer eventually leads to formatting the drive to reset this, irregardless of fat32 or ntfs. I believe this person cloned the drive to another, so he had a working drive with his windows install on it, then wrote zero's to his original drive with the manufacturers diagnostics tools, and then cloned it back.