I've got more data. I used a tool called Tag&Rename on some of my MP3's before I decided that I prefer MP3 Tag Studio. It seems that only the files touched by Tag&Rename have this problem. I've confirmed with Dr. Tag that these files only have ID3v1 tags.

I've tried regenerating the tags with MP3 Tag Studio. I still get the problem. But I did notice something interesting. The status box of MP3 Tag Studio gives a list of all files touched by the last operation. This list is in the same order as Emplode!

(Continuing to investigate...)

-Dylan