Bump, as the issue is still present in 2.48.
Tags that are not recognized by MP3Tag are destroyed upon a save (also see this reported here: /t/10052/1
Also, Florian, can you please add first level atom "rate" mp4 (similar to cprt atom) to allow me to reverse the damage cause by the destruction of the tag? I've been waiting 6 months to fix my files. 