Don't know if this helps, but I have seen some similar behavior. I play 99% FLAC files. I inadvisedly ripped several hundred of these files with EAC set to save tags in ID3 format. I now leave that box unchecked, and presumably the tags are now Ogg or something similar.
Anyway, on the FLAC files with ID3 tags, you can only click Tag Inspector if one file is selected. With multiple files selected, Tag Inspector is greyed out. On the files with Ogg (or whatever) tags, you can click Tag Inspector with multiple files selected, and edit them accordingly.
Other related odd behavior with FLAC files with ID3 tags; if you select multiple artists you will often find a phantom entry is created in the artists "splitter" dialog box. This entry is characterized as "Performer" and contains several - usually all - of the individual artists. You can't delete this, or at least if you do they keep coming back. This behavior is not apparent with "Ogg" tags.
People tell you not to write ID3 tags into FLAC files...