End-turn stuff off the top of my head:
- You can get an event that will lower happiness or destroy buildings that have a happiness effect.
- An AI faction can move spies into your province to kick up unrest.
- Depending on the religious mix in a province, an AI faction's proselytizer can stir up trouble.
- Something untoward can happen to your faction leader or governor.
I try to keep happiness above 120%. This gives me a little wiggle room for the unexpected, and also prevents re-emergences from dragging in my provinces. Don't know why you would see unexplained shifts before hitting end-turn though.

Are ships (and the moving thereof) involved?
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