At first there were some strong evidence that putting droids into a certain slot would permanently lock that troop slot into neutral morale no matter what. But after kicking the droids out of my party and restarting the game (not starting WHOLE game over, just stopping the application and starting it again), my morale problems went away. I haven't had any morale glitches since.
Anyway, now I'm back to just thinking it is glitchy. However, using droids seems to be the trigger for the problems occurring.
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