The same happened to me too a half year ago: i remarked that about 300 tracks lost all its tags. Because foobar2000 still told that tag type is id3v2.3 i looked with a tag examiner and discovered that in allo the files were two PRIV-frames. I am not sure but i think in most, if not all cases complete albums were destroyed. The folders were indexed and placed in windows library. I can insure that the files weren't touched by windows explorer, wmp or windows media center. (all the files were tagged inside foobar with discogs component and manually)
Well then, I'm sure glad I've been rolling with m4a for years... so yeah, I'd recommend setting mp3 files to read-only then.