Sounds more like an issue with your backup. I've used CloneCD, Primo (the original, not RNM), and recently started using DVDDecrypter and they all work fine.
CloneCD on all CD's--use the PS2 settings and image to HardDrive--not one-to-one copy. I've only re-duped a few off mine for friends, but it has worked fine.
Primo for DVD's--build global image on hard drive, then burn from global image.
DVDDecrypter for DVD's--use ISO mode to read image to hard drive, splitting at 2GB (I have Win98SE), then use ISO mode to write to DVD-R.
I always burn my first backup to DVD-RW to test it. If it's a game I'm not sure I want to keep and I have a successful RW burn, I'll delete the image to reclaim HD space and play the RW for a while. If I decide to keep it, I'll image off the RW to make a permanent DVD-R. Never had any problems with it.
If it ain't broke don't try to fix it! But, hell if you can tweak that bastard just a little bit more....hehehe.