This problem has been mentioned before, but i can't remember when or where it was. I've also seen this behaviour in MC, but it's very, very hard to identify when it happens - no-one can keep track of each and every file in a collection, in order to identify any possible, unintentional tag changes.
The effect is what i call "tag shifting". Sometime, certain tags will get changed by MC. Sometimes, tags get swapped (like, for example, year and comment), or sometimes they disappear completely. I've also seen tags "shift", which means that all tags are still in the file, but at the wrong location. An example would be a "Mood" tag that's suddenly a "Situation" tag, and the "Situation" tag is something else. Most of the time, the changes seem to affect single tracks, not whole albums. I've seen this happening very often in MC11, but not as much in MC12. For quite some time with MC11, i was thinking this was an issue with special characters in the database. To get rid of the problem in MC11, i deleted a lot of custom fields (for example, i had a user field with full-text AMG reviews), and rebuilt the database from scratch. After that, the problem was (more or less) gone. From time to time (in MC12), i stumble across a track where the tags have been changed (and i'm pretty certain it wasn't an intentional change), and i just shrug and correct the error. I know all this sounds a bit esoteric, but i'm pretty sure there is some kind of problem, sometimes, with some files. But i have not the slightest idea as to what might cause the problem.
EDIT: ah, i've just discovered one such file. It has a "Situation" tag with the value "Zuhören". The value is duplicated in the "Comment" field, and i'm sure i didn't do that. The tag is still there after "update libarary from tags". Even after deleting the "Comment" tag, or filling it with a different value, the "Zuhören" value will still be there after "update library from tags". And now it gets really strange: i open the file with Mp3tag, and the only tag i see with a value of "Zuhören" is a "Musicmatch Situation" tag. I delete that tag in Mp3tag (and clear the "Sitation" tag in MC), and again do a "update library from tags" in MC. The entry is still in MC! A quick check in Mp3tag reveals that there is not a single tag with the value "Zuhören" in the file. To get rid of the tag, i have to delete _both_ tags in MC - the "Comment" tag, and the "Situation" tag. After that, as soon as i change the "Situation" tag to "Zuhören" again, the "Comment" tag is set to the same value, too. Looks like a bug to me. If i use a "Situation" value without an umlaut, the "Comment" tags stays empty.
EDIT2: for testing, i've searched for other tracks with a "Zuhören" value in the "Situation" field, and an empty "Comment" field. After "update library from tags", both fields show the "Zuhören" value. This is definitely a bug.
steveklein, do you have umlauts or other special characters in your tags?
EDIT3: even more strange effects. Two tracks with a "Chill" value in the "Situation" tag suddenly have the same value in the "Comment" tag. No umlauts whatsoever with these two.
EDIT4: and more of the same... 22 tracks with the value "Deutschland;Nürnberg" in a user defined field suddenly have the same value in the "Comment" field.