I have tried another method - create a Disc Image with the files, to a different drive, and then burn that.
I can't burn the mounted disc image correctly, because apparently one can't span a disc image. So, I opened up the mounted image, and pulled all the files from it to make a new data disc.
Being in a disc image, it would seem that the image would be locked, so no files, even invisible, would be written to or from the image. This would therefore rule out yet another possibility.
The files went through the first disc successfully, but then had mismatches on the second disc, twice. Therefore, three coasters for the unusable set, and I gave up there.
Anything else to try to isolate? It seems that the possibility of files changing along the way has been ruled out.
I'm on 10.0.8 - I know 10.0.9 was released, but looks like it's been pulled. I'm still on Snow Leopard, so I don't know how much the update would matter anyway.