The next time this happens, can you try just moving it around a little bit at the current end of the fader that you are on (i.e. don't go near the middle) and see if it recovers its position? I can't imagine why you would need to go near the center again (though I also have no idea why this would be happening in the first place). You could also try logging the MIDI messages that you're receiving (in the MIDI window of MixEmergency), and see that it is receiving the correct messages (or any messages at all) during these periods.