There are a couple more changes that you should try that have not been mentioned yet.

1) Set your throttle and brake EPA settings on your TX to 120% (or w/e full throw is on spektrums), and then go through the initial programming with the ESC again so it sees the new settings. This made a huge difference in getting my 3PM to work right when I had problems with initial setup.

2) Already mentioned but worth repeating, set your neutral zone to 9% or 12%. If you don't and for some reason your neutrals center position changes the controller will not accept it and fail to start up.

Good luck.

I was woundering about some of the "nitro assist" functions of my radio, ABS and that deal where it opens the throttle differently for the lag on a nitro motor. Any chance the ABS could be cycling into the throttle range? or something along that line that is throwing off the MGM?