Tor Browser ignores bookmark changes after downloading update

The last few times I have updated Tor Browser, it has let me make changes to bookmarks after it downloaded the update, but has discarded those changes after it relaunched.

So every time I update, I lose all bookmark changes between the update download, and the update being applied.

I've used the incremental auto-updater on the released version. I'm now using Tor Browser 5.5 on OS X 10.11.2.