Two quick points:
1) Don't underestimate the apple forums. You'd be surprised who's lurking around in there.
2) I tag all my mp3's with MP3::Tag (both v1 and v2 tags) and iTunes has no problem reading them. I seem to be using iTunes 7.4.1 (2), and MP3::Tag 0.94. Which versions are you using?
In the end, including a code snippet is probably the quickest way to figure out what's going on. It'd also probably be helpful to use Data::Dumper to dump the data prior to setting the tag, and after the tag has been set, create a new tag from the file, dump that, and compare the two. Also, you could append v1 to each of the v1 tags and v2 to each of the v2's. This will allow you to see which tag you are seeing with the other tools you are using to view the tag. It may be that your v2 tag is empty, but the v1 is set, and itunes is happily showing you an empty v2 tag, while the other two apps either move on to the v1, or try the v1 first.