I found that one of the 3 powered USB hubs I used was preventing the system from boot while cold. On a nice crisp -12c morning I started up the car and started pulling USB off the back of the computer. As soon as I pulled the one hub it fired right up. I shut everything down, plugged everything in except that suspect hub, and again it fires up. I left everything for another 2 hours so that it was cold, and again it would fire right up.
I have managed to bypass this hub for now. Looks like a new one in my future.