I have no idea how to diagnose windows problems w/ Knoppix. You can however use DBAN to erase your drive.

http://dban.sourceforge.net/

If you don't have a floppy you could always use Knoppix to zero the drive like so:

dd if=/dev/zero of=/dev/hda

A word of caution- don't test that command out to see what it does. There is no "are you sure?".