This is quite interesting/disturbing.
If you can risk losing one CD-R for testing purposes, I would suggest burning an audio CD using
Burn to see if that gets around the problem, if it is indeed software based.
Otherwise, if you have Toast, I would recommend using that to burn your CDs and DVDs. I have to admit that I don't use any Apple applications other than Disk Utility for burning discs, so it's difficult to pinpoint the problem here. One common thing that Mac users over the years have seemed to suggest is lowering burn speed, sometimes to the extreme that burning takes place at real time! Using my Lite-On drive and Toast, I am able to successfully burn CDs and DVDs at very close to the maximum speed allowed by the medium in question, so I don't think that lowering the burn speed is necessarily a solution.
By the way, did you make sure to set the jumper of your new drive according to the instructions in your Power Mac user guide? In the case of my computer, I believe it needed to be set to Cable Select. I'd have to double-check that, but I think I recall having to do that when I installed it, when it would have seemed obvious to set it to Master.