As you have learned, Windows is not very good for handling tags for FLAC files.
But if you are using WMP, then maybe you'll be interested in WMP Tag Plus:
http://bmproductions.fixnum.org/index.htm?http://bmproductions.fixnum.org/wmpplus/
My understanding is that it won't display FLAC tags in Explorer, but it claims to display them in WMP.
And tags for Ogg Vorbis, WavPack, Monkey's Audio, Musepack and MPEG-4 are also supported.