Yes, the "fill properties" feature IS working perfectly, and I can build new libraries with this procedure as you described. All artist, album, track#, and track-title information (and cover art from the folder) is extracted correctly (and written on tags so that other instances of MC on other computers instantly recognize the information).
My problem was an older library, built by an earlier version of MC, which apparently was confused by multiple "-" characters on the file name and could not write the track# information for those files. I could not add the missing track#s by redoing the procedure, even after erasing all tags (or maybe the program was not able to erase the tags).
Anyway, my solution will be to delete that whole library, and rebuilt it with the latest version of MC; and I hope everything would be fine. I would loose some subsequently added tags but that is not a big deal.
All my files are WAV, btw.