Unknown Error on Unknown File?
 

While scanning with ClonyXXL I received the error:

An unknown error occurred while accessing an unnamed file

What does this mean?

It's rather obvious....

Clony tried to access an unknown file and received an error report in reply that it wasn't programmed to understand.

So does that mean I can't copy the software? Or is ClonyXXL not liking my CD?

Update: Luckily my old scratched CD had no copy protection. I backed it up to a CD-RW and then made a permanent backup on CD-R.

it may have happened beacause as you said the cd was scratched....