Help in Making Backup Copy of Original Operation Flashpoint CD
 

I have a sony CRX1611 CD writer, and was wondering if anyone could please tell me the best way to make a copy of Operation Flashpoint.
I have tried doing a stanard copy using Clone CD, but it wont let me apply 1.1 patch. If I put the original CD the patch works fine, but the game wont load unless original CD is in.
Is there some setting I need to enable when using clone or something?
ANy help would be greatly appreciated.
Thanks