Jap PS2 won't play backups made with CloneCD if you use the Utility Disk to boot with. They have to be made with CDRWin and patched with the Paradox Universal Patcher. That causes problems for protected EA games for which the patches are geared to AR/GS method.

What modchip method do you use?
Does the abpve explanation match your symptoms?
What are your symptoms?