Have you tried restarting SystemUIServer? (killall SystemUIServer) When something like his is happening and restarting the Dock doesn't help, SystemUIServer is the next one to try.


It happened again, and I tried simply closing the MacBook, waiting a couple of seconds, and reopening. Maybe it was a fluke, but it worked. I'll wait and see if it fixes the problem a second time to make sure that it really did something.

This answer is less than ideal, e.g., if I'm in the middle of a big download, so I'd like to wait and see if this answer can help towards a better solution. What does suspend trigger that I could do without suspending?