I've noticed that kid3 doesn't like the way multiple genres are managed by GMB. So much so that it will make it compliant by choosing one randomly and removing all others on save.
I'm guessing that it's because of some id3 specification which bars multiple genres.
I've also noticed that instead of multiple entries "Rock" "Progressive", a single genre entry subdivided by commas "Rock, Progressive" will work with both GMB and kid3. But GMB doesn't have this implemented and so adding a genre in files properties or the right click menu, creates a new genre rather than adding to the existing one with a comma.
It's not a big problem of course, just a hint to make GMB more perfect in case it's a trivial fix and you didn't know this.
So far I've worked around kid3 erasing my genres by adding and then removing a "temp" genre to an entire album/artist in GMB right after I save tags with kid3. This rewrites the genres to the files, as long as it's done before a refresh of the tags in GMB.
At any rate, thanks so much for this gem of a tool :D