Tags on flac not being indexed

[simbun]

The native tag format for FLAC is Vorbis Comments, so I assume that's why it's not reading the ID3 tags.

What tool have you been using to tag your files? I remember years ago a situation where EAC would add Vorbis and ID3 (if you ticked "Add ID3" in the external compression configuration), so it might be worth checking if a similar thing has happened.

The easiest way to check (if you have access to a Windows PC) would be to open an album (make a copy on one) up in Mp3tag and make sure the "Tag" column is showing in the UI, and if both tag formats are there it'll show (FLAC (FLAC ID3v2)).
If this is the case, you can then select all the tracks of the album, "Tag Cut" and then "Tag Paste" and it'll paste back only the Vorbis Comments.

If both formats are there, report back and we'll see if there's another way of addressing it.

EDIT: I've just looked again at your output listing, and I didn't realise that when you said "I tag using id3v2 on debian", that id3v2 was the program, in that case I assume you don't have both, and probably need to look at a way of converting to Vorbis, unless MinimServer can handle this somehow.