In the meantime until someone answers, set up a new rig (with CAT its just a click) add ear bones. Test the new rig to see if it suffers the same malady. If the new rig works (and it should) then try discover the differences between the simple rig and your working rig.
Did you add the ears after you created the animation layer? Could you try creating a new animation layer with the ears and see if it works? I suspect the controllers on the animation layer are not being set if you added rigging after creating a animation layer. m