Steve,
some of your observations resemble what happens if your R3 split point has moved slightly away from its default position. It should be hard up against the other split points, if a slight gap develops (as a result of manual adjustment or a "rogue" registration) you will lose a right hand voice or two where you are expecting 3 voices to sound. Next time it happens suggest you check this, (or check now if you wish whether the effect sounds the same with 3 voices active by manually moving R3 split point a semitone to the right). If you are happy to disable registrations from moving split points you can put a tick in Split Point in Parameter lock after making sure it is set as you want it. (You will still be able to change it manually).
John