Matt, how are you powering the car PC?
If you want, I have a 120W bare board Power supply unit specifically designed for car or boat installation. I used it when I had a car PC for my 206.
You can move some jumpers around on the board so the PC stays on for like 15 seconds, 30 seconds, 5 mins etc after you turn the car off so if you just pop into the shops the PC doesn't have to boot up whilst you buy a pint of milk.
Also has the correct wires to sense when the car has started up and then will boot the PC.
Has sat in my box of parts unused for about 3 years, but it does still work and just thought you may like it if you don't have a solution already.
EDIT:
Just re-read, M2-ATX, that's what I have. Could always send yours back and take mine for a lot less cash