Perhaps you could try using something like Nero CD Speed http://www.cdspeed2000.com/ to check if you can read the ATIP info from a CDR, using the 'Disc info' option, or of course another program that can do this.
If you CAN'T then some other program is hiding it and maybe that's why the original CD won't work?
Just to re-iterate; the Hide CDR Media option in CloneCD tray should be UNTICKED, and the Ignore Media Type in Alcohol should be UNTICKED. Similarly for Daemon Tools if there is such an option? Just quitting the CloneCD tray, won't turn off the Hide CDR media, it has to be unticked. Similarly with Alcohol, even though the main program isn't running the Ignore Media Type still runs in the background.
This also means of course that you can't run the back up from a CD Writer which will reveal the ATIP info!