If your USB drive is formatted with NTFS, them you have likely corrupted the NTFS partition. Knoppix can not safely write to NTFS (There are those who believe otherwise, but I've seen too many posts of problem to convert to their beliefs). I would not ever use a NTFS drive that Knoppix has written to until I completely reformat it.

If it is a FAT partitioned drive then were you careful to unmount the drive before moving it to the other system? You must unmount a Linux drive before disconnecting it. (You would have to do this with a NTFS drive too, but that hardly matters since the drive will be corrupt before you can unmount it).

Personally, I recover files with Knoppix by installing a FTP server on a Windows box, and use Konquror under Knoppix as an FTP client on the recovery machine, transferring the files across a network. There are many free FTP servers for Windows that can be used for this. There are many other ways to recover files also, no one solution is right for everyone.