I'm pretty sure that if the ID3 V2.x tags contain "non-standard" parts, emplode will get confused and not parse anything for that file, when you're uploading.

What I do now is clear the existing ID3 stuff, and re-gen it all. There's a fantastic, free program for this: http://www.id3-tagit.de/

Only possible downside is that it requires dot-net framework 1.1.