Troubleshooting problem with file numbering display

[simbun]

You don't need to worry yourself with what Vorbis Comments are, it's just the default tagging format for FLAC (and OGG) just like ID3 is for MP3's.

I'd add DISCNUMBER to the missing files and then perform a rescan to see if that fixes the problem, if not then try and do the same with ALBUM, and finally ALBUMARTIST to see if that fixes it.

I'd keep a backup of the files whilst doing this just in case you want to get back the original files for some reason.