Something in Windoze is interfering with hibernation.
Could be an application, a service or a driver.
So I got everything installed and have it all working great except the ignition off settings. I have the jumper on the M2 set to 5sec/2hours, and today I had it off for around 3 or 4 hours and it was still hibernating when I started my car. Is this normal? I thought the M2 would shut the pc off after 2 hours?
If its hibernating when you turn the car off then the windows power settings are correct.
You need to figure out what is preventing the hibernation like DarquePervert said. Best place to check is the windows event viewer to see whats crashing or hanging.