There are two totally different methods for tagging FLACs. The first was using ID3v2 tags, just as if it was an mp3. The second way is to use the same tagging method used on Ogg Vorbis files. This came about when FLAC was incorporated into the Ogg project. It's unclear if the FLAC has to be Ogg encapsulated in order to use Vorbis comments. My guess is that it does. I'd say that if you have a raw FLAC file, the best comment method to use would be ID3v2, but that doesn't mean that's what your tag.exe program does.

Try opening up the FLAC file in a text editor and see if you can see the title, et al. at the beginning. If you see TIT2 and TALB mixed in there, too, it's ID3v2, otherwise it's probably Vorbis comments.