I'm pretty sure that when using a USB mod the game has to be EA patched anyway regardless of whether you've used clone cd or not.Also when making a bin image with CDRWIN make sure to untick the RAW mode box (most of the EA patches are designed to work on a non RAW image). I know this to be a fact because when I switched froma NEO 2.2 to NEO 4 I had to re-copy & patch every EA sports game I owned(all the original copies were done with Clone CD from originals & they still didn't work)
Hope this helps.
If you can't find the patches you want on psxcopyworld try
www.gamefreax.de
It has a pretty good collection.