I've seen many times that when rebooting the board, or connecting the APM +5V rail when connected through USB, we can loose CH1 or 2 or 3 or 4 input.
This is caused i think by a PPM encoder crash because of noise or spikes on the +VCC rail.
Eventually the PPM encoder could be crashed by the main AVR reboot noise.
After watching to the APM schematics, it seems that the PPM encoder reset is not connected to the reset switch, neither to the USB reset output.
To avoid problems, i think that the PPM encoder reset input should be connected to main board reset circuitry so that it is resestted at the same time when USB connection is done or when manualy reseting the board.
Perhaps that the USB +5V shoud not be used as well, to avoid power spikes when connecting USB and crashing the PPM encoder.
Those PPM crashes could explain why some users do have strange radio behavior sometimes.