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.
i have some questions? is it always the same esc or chennel output.
the other thing i notice is your feeding all 4 esc powers into the servo rail. usualy there is only 1.

Well spotted, Michael. Mark: you need to be connecting the ESCs via a power distribution board, which just connects one of their BECs. If you connect all four BECs they're going to fight.
Hmm interesting because I'm using the 3DR dist board and am having the same issue

Michael: different motors; some will work periodically; one always stays off.
Chris: just tried disconnecting the power from three of the ESCs, no joy, symptoms are identical. (Although now I understand the reason to have power from just one, so that a voltage differential between two BECs doesn't cause a continuous power drain).
I'll make a permanent fix later, but for testing I just made these connectors and put them between the ESCs and APM:
Comment by Vishal on December 31, 2011 at 4:39pm We've been discussing the issue in this thread. However for me, I already have a properly functioning power distribution board in place which works fine with APM1.
This workaround of plugging in the board to power first is usable temporarily. But I think we need a more permanent way of arming the esc's. This issue never existed on APM 1 so the problem is something with the board or the new code.

Yes, the same configuration works well with an APM 1. Still investigating, hope somebody else might have some insight as well...
To others who are seeing the same issue, is it also happening on just one motor? Does it happen on any motor besides motor 2?

In my case: it always happens on the back left motor, and sometimes on the back right or front right motor. The front left motor has never had a problem. I'll try switching the ESCs to see if the problem is following particular ESCs around.
Comment by Vishal on January 2, 2012 at 2:12pm
Comment by dudz on May 14, 2012 at 7:54am On my Y6 I have 4x Hobbywing 30A esc's, and 2x the same brand and tech but they have two capacitors instead of one (newer model)... I have this issue with the two new model ESC's on channel 5 and 6. In CLI under setup/motors they all spin except these two. I calibrate them again.....same problem, even with connecting the lipo after USB and motors command. If I start up without MP and just lipo to fly, they arm ok. Am I missing something ?
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