I have not seen reports of this problem before. What happens when you boot Knoppix without the external drive attached? What type drives are they and what interfaces are being used? That is, is the internal drive IDE or SATA or something else? Is the external drive connected by USB, Firewire, SATA, or something else?

I have seen many cases where Windows corrupts a drive so bad that Knoppix can't recover it, but that still doesn't explain the external drive showing up twice.