I'm using APM1.4 hardware with ArduPlane V2.74b firmware and a Spektrum R/C system.
When I switch between manual & stabilize modes the throttle output changes.
If throttle is at minimum in manual [ 1089 micro seconds ] , switching to stabilize causes it to increase to [ 1173 micro seconds ]
If the throttle is at maximum [ 1921 micro seconds ] , switching to stabilize causes the output to drop to [ 1838 ]
Returning back to manual mode in either case returns the throttle output back to the previous value.
I've tried this with the throttle at many different settings and it seems that in stabilize mode the min & max values become 1173 & 1838 respectively.
The radio calibration has been done and the min & max values stored in the APM parameters do match the radios reported output.
I thought that the throttle output was supposed to be completely manually controlled in stabilize mode.
These changes in the throttle output are visible in the Mission Planner tuning screen and I have measured the pulses with my servo/receiver tester.
Also, I have observed some glitching once in a while in the airplane's elevons when switching between manual & stabilize.
Currently, for testing purposes I have set all five user flight modes to stabilize, so APM isn't momentarily engaging in another flight mode when I'm switching flight modes.