Hmm, any ideas of potential causes? Are there any conditions that must be met for it to save? If so, I'm not fulfilling them.
I played three very short tracks (3-5 sec each), waited a few minutes, exited MusicBee properly at 16:26. MusicBeeLibrary.mbl saved at 16:26, nothing lost.
Next, I played three other similar tracks, waited for >20 minutes with the music paused/not touching MusicBee. At 16:58 the library was still last modified 16:26, so as expected the plays were lost when forcibly exiting MusicBee.