Hello, I notice that in some case, the metadata were not competetly cleared even with the option enabled.
In the tags options, I have enable "write tags to file", "clear existing tags", "remove id3 tags from FLAC files", "Remove APEv2tags from MP3 files", "Tag Compatibility 2.3", "ID3v2 Text Encoding UTF-16".

You can find the files that are causing the bug to appear at:
http://nicolas.cenerario.free.fr/bugged.zip
There are 6 files for 2 songs.
For each songs, the music data of the three corresponding files are the same (I made a byte-to-byte comparison after removing metadata from each files to verify). This mean that the only differences are on the metadata. But when I import the files into MusicBrainz Picard, the metadata are the same. I suspected the embeded pictures to be the cause of the differences. With the options I enabled, I expected that saving the files from MusicBrainz Picard would correct the metadata (including the embeded pictures also) but it didn't. In fact, I noticed that if I removed all metadata with MusicBrainz Picard and saving, it was working: the duplicated files were indeed the same, but if I left too many metadata, it was keeping something making each files different even if everything were supposed to be the same.

Since, the only "invisible" metadata were embeded pictures, I tried to remove them with another software (foobar 2000 which as a function to clear embded pictures), and indeed the files were identical as they should be. But maybe foobar 2000 is doing something else than just removing embeded pictures so, I'm not sure it is perfectly relyable.

I might have found a patch and a discussion has started on GitHub : https://github.com/musicbrainz/picard/pull/395

Thank you.

PS: This bug might be related to: #PICARD-466 Existing tags not cleared