I know I may be quite late here, but;
have you tried booting Windows into Safe Mode (F - or tried Booting from 2K/XP CDROM ? (set BIOS to boot from CDROM as 1st in Boot device order).....are you using NTFS ? You likely need to access Recovery Console on the CDROM and Run CHKDSK C: /r on your HDD to repair any corruption if possible.

In trying to keep this from becoming a WIn support thread - Knoppix can see all files, but for some reason you may have those contents of \<userprofile> "encrypted" possibly ? If so, AFAIK knoppix won't help you there. Are you sure you're allowing viewing of "hidden" files?