Update:

mp3tool showed these files as having a bad vbr header.

I fixed the header, and re-uploaded. Music is fine now, including the DVD rip.

Why would the timecode header effect the music?

Now I've got to go write some more perl to download the files off the player, run mp3tool --repair on them, and then upload them back on. I'm sure that over 70% of my music is going to be like this, as most of them were encoded at the same time. What I don't understand is why it's effecting like this.