+1 for improving this, still, though I don't believe autosave after e.g. 20 minutes is the solution. The solution stated by Steven above sounds perfect, but it doesn't work that way for me! I'm on version 3.2.6902 and am still having issues.
For example, I changed the rating of a song at 21:47. At 21:54, after playing a couple of other songs, I killed MusicBee, and that rating I changed was gone.
I have MusicBee set to store ratings in the database, rather than in file tags.
Earlier today, I changed the layout of "Upcoming tracks" to show the track rating below the time, clicked Apply and Save (as I always do).
Hours later I killed MusicBee, and that layout change reverted back, so settings can also be lost. Just to test, I made a similar change, clicked Apply, clicked Save, waited 2 minutes, and killed MB. Result: the change reverted back to how it was before.
Simultaneously with the "crash" mentioned earlier, I lost ratings on at least 20 tracks, along with "Last played" info and play count for more than the entire day, with the most recently played song being shown as yesterday afternoon -- I've been listening most of the day today, and all evening yesterday, so that's definitely not correct.
This exact issue of losing ratings etc. is why I switched from foobar2000 recently, so it'd be awesome if it could be fixed here (again?).
BTW, if anyone's wondering why I would kill MusicBee, the answer is plugin development. I've changed my build script to not kill it by force, but regardless, this issue will also bite people when computers crash, at power outages, if MusicBee crashes (hasn't happened to me) or perhaps during Windows updates, so IMO it's worth the attention.
UPDATE: I noticed there are 3.3 betas available, so I installed the latest (3.3.6962).
I played a few full songs, so there were >5 minutes for the first play to count. I also changed a rating as I started the playback, and the contrast for a text in the upcoming songs panel, followed by Apply and Save.
So about 10 minutes after those changes, I killed MusicBee, and everything reverted back.