<snip>
...it can't find a CD with Knoppix on it...
</snip>

Hmmm... if you were able to make a boot floppy from the CD, the system SHOULD be able to find the CD. If the CD directory can be read under Windows, and shows a directory called "Knoppix" (and not just one large file with a .ISO extension) then the CD was mastered properly.

It's possible that a mastering glitch or fingerprint is keeping the table of contents (TOC) from being read correctly. Try making another copy and see what happens -- and/or look closely at the data surface of the "bad" CD for scratches or fingerprints. One of the drawbacks of a disc full of data is that they are harder to handle; even the slightest fingerprint will cause problems.