I think I may have misunderstood the problem. I was thinking you were getting errors from the hard drive. I was also thinking that you could boot to the cd fine and see files, but not access all of the files.

Now I'm thinking you have a specific partition that you can't reach and two operating systems are seeing it as two different file systems. I've never had any problems getting any data that is still intact on the disk with a knoppix disk. I just copy my files over and get out, if you can't do this I'd question whether or not the data is still physically there anymore and if it can be recovered without the use of special (non-software) tools.