I believe I found a similar bug. After saving a new Comment field with TagLib, Mp3tag no longer detects an MP4 tag in my file. iTunes and foobar2000 (and TagLib) can still read the file.
Looking in the file with a hex editor, it appears the tag data is all still there, so it seems Mp3tag is breaking where no other major player is, when attempting to read an MP4 tag.
I can send a sample file (before and after) to the developers (Florian or someone else?) if needed. This also affected Mp3tag 2.55a (I'm now using 2.57 which also can't find the MP4 tag).