I have somewhat of a similar problem although mine do not screw up like yours al of the time. I usually jusy reset and it all gets back to normal.
One of my maracas is broken, although the other works fine and it seems the base doesnt have a problem with it. I ordered a single marca which should be here in a couple of days, When I recieve it I will be able to clarify whether it is the base or the maraca casuing the trouble. Do you know if I can use the controller extension with the maracas?