The exact same thing happened to me, I emailed Native Instruments and they told me what to do to fix it and it worked.
Are you loading tracks directly from Itunes? If so, you shouldn’t.
You should create a Traktor playlist. So just right click on ‘Playlists’ (below Track Collection) and ‘create a new playlist’ and then drag and drop the songs from your itunes to your new Traktor Playlist. Once you play a song the BPM’s should then save.
