I took my modified Elev-8 out for a flight a few days ago and it behaved strangely - would not hold position in Loiter mode and and started to fly way when I switched to RTL, so I had to take over and land manually. I pulled the flight controller off and opened up the case to make sure that the barometric sensor had a piece of dark foam covering it (it did). The barometric sensor is sensitive to light and wind, so it must be covered.
Anyway, I sealed up the case, re-flashed the firmware and went through all of the calibrations but during power up, I was getting an alert: "Pre-arm Chack FS_THR_VALUE". IN the past, I had occasional arming problems - the error was "No RC" even though the transmitter was on and the aircraft was responding to the arm command. Well, I finally found that all of this was related (except the Loiter, RTL issue, which got solved when I re-calibrated the compass).
It turns out that my flight controller (APM, and I also suspect Pixhawk), monitor channel 3 ( throttle), to determine whether or not the aircraft has lost contact with the ground station. Then the aircraft flies out of range of your transmitter, the receiver will behave differently depending on the kind you have. The cheaper Orange receivers may just continue sending the same signals to all channels when contact was lost - this is a bad thing because the flight controller won't know that anything is amiss. Other receivers, like mine (Orange R615X), will, after a second, send the signals on all channels it saw during the bind process.
In order to get the failsafe to work properly, you need to monitor the pulse width when the throttle stick is at its lowest position - note that value. You then can lower the value by using the throttle trim. So say, for example, the the throttle minimum value is 990; using the throttle trim, you can lower it to, say, 950. Now, rebind the receiver with the transmitter sending this lower throttle minimum value. After binding, reset your throttle trim back to the mid setting, and set your throttle failsafe value to something between 950 (lost signal value) and 990 (minimum throttle setting when transmitter is on). I was getting the pre-arm alert because my failsafe value was set above the minimum throttle setting when the transmitter was on.
You are all set. You can test by arming your aircraft while on the ground and then turning off your transmitter - the aircraft should disarm.
After going through this exercise, my quad arms when I want and I no longer get any mystery alerts. I have not actually tested the failsafe - will need to go out to a large field and turn off the transmitter while it is flying - a scary exercise! But I will do this and I will also repeat this process with my other two quads.
I know that this is APM/Pixhawk specific, but I suspect that the same general princicple applies to other controllers that have a groundstation failsafe option.