Strange, there are a couple of things I do differently, but I'd not think it makes much difference.

1) I only replace the individual files that have changed, not the entire directory.

2) I burn the disk directly from UltraISO, but I have used Nero to burn as well and both work.

Other than that, I can't think of anything else to sugest, especially as you've rulled out the DVD writing itself by creating a standard disk.