When I´ve copied the Rainbow Six Ghost Recon CD with Clone CD, all the files are there and everything worked fine in the copying-process, but when I want to start the game it tells me to put in the CD and try again… WHY ?
Please help me with this problem 
Apparently your backup is not perfect. The copy protection that is on the original was not copied properly. Be sure that your writer is compatible with CloneCD and you use the latest version with the righth settings.
Perhaps these links help you a bit:
http://club.cdfreaks.com/showthread.php?threadid=40293&highlight=ghost+AND+recon
http://club.cdfreaks.com/showthread.php?threadid=39303&highlight=ghost+AND+recon
http://club.cdfreaks.com/showthread.php?threadid=37729&highlight=ghost+AND+recon
The last resort is applying a patch, but that would be illegal and I can’t help you there on this forum.