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I created a new issue about this a couple of months ago.
Basically, JAudioTagger does not handle mp3 files that well. Fortunately, I've found a good work-around. The trick is to remove both ID3v1 and ID3v2 tags, create new ones and then add them to the audio file.
I found this trick while developing my own program for tagging audio files called SongTagger.
Here are the mp3 files downloaded and tagged after this fix:
P.S. youtube-dl needs updating