Thats because the clone tray is running in the background at all times, even if you disable it thru their tray it is still running and will until you go into msconfig and shut it down. So to test your clonecd version again go to msconfig and then the startup tab and shut down the clonetray that way restart and see if the back-up still works in the plex. my guess is it may not.

If he is not hiding the atip then the copy will not work in cdrw's at all, no where in his testing on the clean system does he say he is using anything to hide the atip, so we know the back-up will not work.