If you're unsure of yourself, you may want to head back to Cartronics to do some troubleshooting.
A few questions:
1 - How do you have the M2ATX wired up? The common configuration is constant 12v power (straight to the battery), ground and an ignition-controlled line. This third line senses the power state of the line to trigger startup & shutdown of the PC.
2 - What gauge wires are you using for power and ground?
3 - Have you (or your installer) confirmed the voltage you're getting on the 12v constant line and the ignition controlled line with key off & key on using a multimeter?
4 - How are you certain that the motherboard is getting power? Did you measure the voltage at the 20-pin ATX connector with a multimeter?
This is a reason I would not recommend having a shop install a vehicle PC unless they are knowledgable and/or experienced in installing PCs in vehicles. You can give them the wiring diagrams and say "install it like this", but unless they know how to troubleshoot a PC, you have no recourse other than to trust their installers.
Add into that the time & money it will cost to work with them to troubleshoot, and you could EASILY have learned how to do this yourself.
Before I got into this I had not installed anything more than a replacement headunit and speakers. Now I understand more about what's involved. With the help of some good informational/educational resources and some knowledgable friends, I'm pretty configent I can install darn near anything electrical in a vehicle.