Probably a little late to this topic, but it's worth pointing out that it looks like anything pre-composed should not be using the Ray-traced 3D renderer either. Even if there is nothing in the scene that uses those features, it will still deactivate multiprocessing. Make sure all your nested compositions use the Classic 3D renderer.
A little frustrating, but maybe can be addressed in an update or future version (hello, CS6 subscription updates?).
