Sorry, didn't think format mattered here. Anyway, AFAIK all of the problematic files are .WAV files. The MP3tag developer has one of the misbehavings files now.
Converting from .WAV to FLAC, etc. doesn't say much more than the conversion can be done. The resulting file will be a new file. The problem is with old, somehow "infected", files. FWIW, I used Audacity to export an "infected" .WAV to another .WAV file (that is, Audacity opened sick.wav, and exported it as not-sick.wav). No problem with tweaking the tags in the exported .WAV, only the source files has problems.
I share your mistrust of .WAV tags. They are often a moving target unlike, for example, .MP3. Oh, well, I'll let Florian (developer) see if he can turn up something. Oh, the joys of modern technology! LOL
Some days I have no idea about what I'm doing. Other days I wonder why I'm doing it.