Sorry for the new post, but this seems worth mentioning:
First, doing a rescan is not refreshing the main panel. Is that intended?
Second, in steps:
1. I open the tag editor for a track and tick "iTunes Compilation."
2. I save in the Tag Editor, and MB reports that 1 file has been updated.
3. I look at Tag Inspector and confirm that iTunes Compilation is set to 1.
4. I rescan the file.
5. When I open the tag editor, iTunes Compilation is unticked again, but Tag Inspector reports that it is still in the file. MB does not treat the track as a compilation.
So far I can only see that this is happening to iTunes Compilation, but I can reproduce it with any track. The iTunes Compilation tag CAN be completely removed through the Tag Inspector.
If it matters, I do have "detect iTunes compilations" ticked in preferences, and the compilation album artist is used in my naming templates. Setting "iTunes Compilation" causes the Album Track Count (also used in a naming template) to be 0, because it changes the album artist.