You can find out what version MusicBee is writing to by looking at preferences, as shown here:
You can find out what kind of tags are currently in your files by using the tag inspector, which is accessed from the Edit screen as shown here:
You can check for ID3v1 tags, for instance, by clicking the radio button for ID3v1. If you find that you have tags in both ID3v1 and ID3v2 for some files that might be why you're losing your work, because MB is rescanning old tags instead of new ones.
Does that help?
(Steven has changed it so that in the latest version, editing your tags with "also save as ID3v1" unchecked will clear the old ID3v1 tags. If you're seeing changes reverted in MB version 2.1.4770+, I'm at a loss)