Without the door/window contact connected to the M1 the M1 is responding correct so you can re-connect those sensor back to the M1. Using the ElkRP2 software under the Status screen when you open the zone the voltage should change and remain in that state until you close the zone. If you do not see a change in voltage then that sensor or even the wiring going to that sensor might have been damaged by the lightning strike. You should try replacing the sensor and retesting.