I imagine this has something to do with ID3v2.3 vs. 2.4 or something, but I'm not sure.

I have noticed the same problem and I believe that is exactly it. I think id3 2.4 is fairly new and some stuff doesn't like it. The id3::tag perl module that I use in my tagging scripts has the same problem. I just use version 2.3 tags to get around the problem. You can have iTunes batch convert all your tags down to 2.3 if you want (look for Convert Tags under the advanced menu).

-Mike