How is the M1ATX wired up?
do youy have the two-wire lead that goes from the M1 to the power switch headers on the motherboard? Have you tried reversing one end of that lead? Polarity matters on many motherboards.
Have you tested the lines that go to 12v constant and 12v switched to make certain they provde 12v constant and 12v switched (by the ignition)?
I suggest breaking out the multimeter.