Same thing happens in my 5D2 since day 1 with ML. It just happens to me in LiveView when I use the joystick to move the focus square. It gets stuck, the focus square keeps moving until the end of the frame and then, after a couple of clicks in the opposite direction or waiting a couple of seconds, works normally again.
It happened with all ML versions I run in the 5D2.
It happened with all ML versions I run in the 5D2.