Rigidbodies stopping Root Motion of animations

I'm unsure why, but a project I'm working on it appears that rigid bodies are not fully compatible with Nav Mesh agents / animators.

I've used them before in this way without problems, but today they started breaking.

I have my agents do this patrol;

1. Go to Point A

2. Rotate around to face the way the agent just came

3. Pause for 5 seconds after rotating

4. Go to Point B

5. Rotate around to face the way just came

6. Pause for 5 seconds

7. Repeat

I need rigid bodies because I'm using triggers (though I am considering ditching triggers and using distance calculations against every agent in the game) but what happens is it starts the turn animation with root motion (Unity's default animations). However after some time, it just stops turning.

I've set the NavMeshAgent.updateRotation to be false. I've set the Rigidbody to kinematic, I've even turned on all Rigidbody constraints (and off again) but that hasn't fixed it.

The only way for me to fix this issue, is in the Editor toggling IsKinematic on/off again. Previously I had IsKinematic permanently on, as I didn't want any physics at all applied to anything. But for some reason my AI started falling through the scene despite Use Gravity being disabled, AND being set to Kinematic.

I'm at a loss what is causing these issues, they seem random and to defy logic. Anyone got any insights?