I’m animating my character doing a somewhat like somersault action, with cog control rotating over 360º forward. Also I’m having followAlign ON so that I can adjust the upper body without affecting the arms orientation. Unluckily my character’s arms flip when the body is about to turn over 180º. Stewart of AM has the same problem, though.
Having a look, I see one of the rotation values of the orient-constrained joint jump suddenly, either from 180º to -179º or -180º to 179º. Interestingly it doesn’t jump visually. But sure it will if you are using the value directly in your setup. So my solution is to use the rotation channels of the actual control ( the upper arm FK controls in my case ), not the orient-constrained joint.
My case is not very common actually. It’s great that the fix is simple. Having too many compromises while animating a character could be frustrated and not fun at all. Moreover, this is not something crazy to do to a rig yet.