I'm seeing this behavior in the tag panel, the column view, and the Extended Tags panel: When trying to create an ORGANIZATION tag in a FLAC file, the value is written as a PUBLISHER tag instead. If there already is a PUBLISHER tag in the file, the value entered for the ORGANIZATION tag is added as an additional PUBLISHER, rather than overwriting the existing PUBLISHER tag.
In the Extended Tags panel, creating a new ORGANIZATION tag looks like it works as expected, showing the new ORGANIZATION tag in the list, but when I save the changes the value I entered is written as another new PUBLISHER tag again.
Everything works the way I expect it to on M4A files, I'm only seeing the issue on FLACs.
Mp3tag is behaving properly. For FLAC files Mp3tag follows the tag list specified for Vorbis Comments. That list does not contain an ORGANIZATION tag. But the PUBLISHER tag is supported for FLAC. It must appear only once per file.
See the "Standard Tag" section on this Vorbis Comments page for the list of allowed tag names.
UPDATE: that linked list is out of date. This list from XIPH.org is newer and it does include ORGANIZATION. So your problem likely involves mapping, as Ohrenkino suggests.
See the mappings in
Ctrl-O > Tags > Mapping
That was it, thanks.