Sounds like you have a very expensive R/C fan!
But, seriously, I can't think of any reason it would do this other than firmware problems. Even then, at least a few others would have the same problem.
Is it possible to program the controller for brake only???
Contrary to my title, I'm not trying to be a smart-ass. I'm just thinking through my keyboard...
Have you tried setting the defaults and reprogramming it?
Also, did you use the CL to program the MMM before syncing it to your transmitter?? I have no idea if it makes a difference but it may be worth trying it the other way.