"Yup - still have this issue with the newest release no matter if we do accel or mag calibration. Happens no matter if GPS is plugged in or not. "

"Problem solved: This was the problem solved by the newest version of Arduplane: 3.5.2. We were having the memory issue on boot and therefore couldn't use any aux pins. "

"Hey - so found out it was an error on boot:
"Unable to open /dev/pwm output 0"
That ArduPilot was spitting out. Not sure why this error was occurring, but a full system reflash (to the newest version in the github) fixed it! :P
Does anyone happen to…"

"Ok - so we'll switch to the external power module then. However, some things are stil left unexplained that I'm concerned about. 
a) Why didn't we need to re-arm if the Pixhawk restarted?
b) If we have dips in power, do you think that would be…"

"That is the servo rail voltage? We measured it with all the servos pulling max Amp and it was steady at 5.5V (with the same battery, once we got back to our lab). 

Edit: In addition, if it was a power reset, then why was the plane still armed…"

"As per here, it can go up to 5.7: http://copter.ardupilot.com/wiki/common-powering-the-pixhawk/. We're at 5.5. "

"Another question - do you think adding a zener diode of the servo voltage lines ould help us at all? It says to do so in the manual. "

"Hmmm - I took another look at the log files (specifically the throttle output, RCIN C3). We do a ton of throttle run-ups, but it doesn't look like there was a throttle run-up right at the at the end of the log. The throttle was at 100% at takeoff -…"

"Haha - we test our transmitter from a full runway length before launch. We've learned that from experience too.  :P

We were on high power at launch - I checked it myself."

"We have two batteries - one that runs the motor (throttle) and another that runs the servos/pixhawk/payloads to ensure that this can't happen.

Also - the pixhawk didn't reboot during takeoff, it just wasn't sending and RC signal (it actually looks…"

"Yes, we have a BEC that just powers the servos and the Pixhawk (it is set to the ok voltage for the Pixhawk, something around 5.5V). Also, the BEC is rated to the max Amps of all the servos (assuming each servo stalls). "