I have a similar question.
I have 2 cdrom drives. In one of them I had the Knoppix disc, in the other I put a blank cd.
I wanted to make a copy of Knoppix with k3b. Simulation went fine, but after the burn process I couldn't boot from the copy. It gave some error and shew only 4-8 basic shell commands are available, so, the copy process failed. Could it be because knoppix was running from the source drive? Although I didn' launch any application while making the copy.