I had an issue with one of mine that sounds similar, but not exactly the same. Mine would cut out and loose control of the port engine intermittently at about 1000 rpm. When it cut out it would automatically shift to neutral and return to idle. If I shifted the lever to idle and held down the button it would regain control. Not fun when I was coming into the dock. The way it works is that depending on where the lever is, it sends a variable voltage to the controller. Something like 4-12V depending on the position. If the controller ever sees 0 Volts, it automatically shifts back to neutral and brings it down to idle. My controller had a little dead spot in the resister that would cause it to trip if I lingered on it. I took it apart to see if I could just replace the resister part, but I was too chicken to try, it would have had do be unsoldered from a printed circuit. I ended up buying a new lever controller and it fixed my problems. Not sure why it would kill your engines and not just put them in neutral. Yours must be set up different than mine are, as the Microcommander can just do shift and throttle, but can't turn the engines off on my boat. If I misunderstood your problem and you just can't start your engine, it is probably because the control box is not seeing the right voltage, so it thinks that the shifters are not in neutral. It has been awhile since I worked on mine, but I think you can read the voltage they are seeing off the little red display on the control box.
