Both Andreas and I had the same problem... fortunately he had it before I did, and had figured out a workaround.
Problem: when powering up, not all motors will spin.
Workaround: apply power to the APM2 before attaching the main battery. You can do this either via USB or by attaching a spare battery/ESC to one of the output lines. As soon as the board boots up, hook up the main battery and remove the second battery.