I may not be any more help, though I have no trouble booting and running Knoppix v3.2 from CD on my laptop.
Does Knoppix load a splash screen with boot:_ when you have the CD inserted and reboot or start your computer?
If so, what do you enter at boot:_ if anything at all? Just hitting the Enter key boots Knoppix for me.
Afaik it will NOT boot from the secondary master (since it's not installed), unless of course, the secondary master is your CD-ROM drive.
What are your 2 hd's - is one primary master and the other primary slave? And what image did you download to create your Knoppix CD? Surely someone will read your posts soon and provide expert advice.