just in case you didn't see this thread:
i am pretty sure that if you use mp3tag to edit a FLAC that has an id3 tag in it, when you save your edit it will remove the id3 tag from the FLAC. this is because its basically considered a hack to put id3 tags in FLACs, and my understanding is that thats also true of putting them in wavs.
i don't know to what extent, if at all, mp3tag will support editing wavs, and/or removing id3 tags from them like it does for FLACs, but i suppose you could experiment.
i think my solution would be to convert the wavs to FLAC, (which should strip out any id3 stuff), and then tag the new FLACs with native FLAC/vorbis tags. (and you could convert back to wav, if you really wanted the files as wav)