While I'm reasonable sure that F-prot will work to detect and repair windows virus on windows partitions from knoppix, I can't find anything on the f-prot website to confirm it. The virus definition files seem to be the same for window or linux etc.

I know that it claims to find suspicious files on windows partitions but that does not mean the company endorses it per se.

Perhaps you could inquire here: http://www.f-prot.com/support/contact_support.html.

Let us know if they respond.

Regards.