Can confirm it doesn't work.
I used Picard from musicbrainz, and sure enough there is a version of fpcalc.exe in the folder, so... I tried copying this one in the musicbee folder ?
Still doesn't work, at all. I tested a popular song (Green Day - American Idiot) in Picard, it instantly found it. With Musicbee ? Keep telling me there's no match for artist.
So i suspect that musicbee isn't even attempting to use sound signature at all, and instead search for "unknown artist" which will of course get no results.
I just d/l Picard Portable 2.44 and can also confirm your results--the songs that would not ID with fpcalc in MusicBee, DO identify in Picard using fpcalc.
Some communication needed between fpcalc.exe and its MusicBrainz sound signature database has been broken somewhere along the line in one of the MusicBee updates. This should probably be moved to the "Bugs" forum.