AFAIK Knoppix only scans for partitions, writes them out in /etc/fstab then proceeds loading whatever it needs. Of course that's true for Knoppix-STD and since there's been a while since I've used the 'simple' Knoppix that might not be the case. However there should be no obvious reason why Knoppix would interfere at all with you HDs, and in Knoppix 3.3 you had to mount NTFS drives with read-write access manually [not sure about 3.4].

My solution with this would be to try a[nother] LiveCD distro, like Gentoo or PHLAK and get your files out somehow. Alternatively you could remove the HD and try using it in another computer - if one is available to you.