Couple of questions first;
Is the HD new, or did you have some version of Windows installed on it before? If you had a previous installation, then rest assured that even with a reasonably thourough wipe, you didn't manage to clean up the drive. MS has stuff written to your drive in sectors that you can't get to normally.
Second question is what procedure did you use to wipe the drive? to escape the MS protected junk, you'll probably need to use a utility from the drive manufacturer to do a low level format on the drive. This is about the only way I can think of to clean up except going in with a set of floppy disks with DOS 5 or thereabout and doing a full format with those. In either case, it's a pain and I'll wish you good luck.
L