It sounds like you do not have the power supply hooked up right and you need to have the jumpers set right.
You really need to get the directions for it and use them.
You need to have it hooked to the power switch socket on the mother board so it will turn it on and off for one.
You also need to make sure that your system is set to shut down when the power button is hit because the M2 will act like you tapped the power button to shut down your computer.
The directions will tell you what the proper settings are for the jumpers.. One setting never shuts off the computer and you have to shut down with the shut down command or remove power from the power supply.
The normal operation for the M2 in a car is to give a shut down pulse to the power button and wait for the computer to shut off or it will shut off anyway a few seconds later. The jumper settings will set this up and you have to read the directions to know for sure how to do it.
I believe mine is an M3 ATX but should work the same way.