That makes it sound like the controller is turning the pump off, does the A/C-Heater fan also stop? Because the controller will turn off the compressor if the ECU tells it to (like because the engine overheated, or because you pressed the accelerator down hard to pass) but it won't turn the blower off. This would imply to me that a condition is sensed by the controller or ECU that meet the requirement of turning the A/C off as part of passing another car (needed all available power to the wheels), or because of engine overheating - disabling the the pump for a reason (maybe there is a sensor somewhere LYING to the ECU or controller).

If the blower is going off as well, that sounds like a physical issue with the controller; a fuse opening up, bad connection in a wiring harness, etc. There is no scenario I am aware of that ALSO turns the blower off if the A/C must be disengaged. If the blower dies as well, I'd bet on a physical issue with the controller itself (the two boards that, it sounds like, you have already inspected).