I read over this know issue:https://github.com/diydrones/ardupilot/issues/1661
I have a slightly different RCmap issue with a pixhawk. I removed my spektrum satelite (no issues just wanted better range) and installed a S.bus receiver. I connected to the mission planner and as expected the channel mapping was off now. I went to the RC map parameters and entered the new channel values and clicked save. I went back to the calibrate Rc tab and both my throttle and pitch were moving even though they had different number values. After entering, saving and testing different values for my throttle, aileron, and elevator I could not get the correct combination. I started changing and saving a given value(say throttle for channel 3) disconnecting mission planner, power cycling the pixhawk, and reconnecting and they would be on a random channel 1 -3 some times two on the same channel.
I decided the s.bus was not fully supported yet and to go back with the spektrum satellite. I put the original spektrum map( i wrote them down originally before changing) in there. In the rc calibration screen everything was moving correctly so I did a transmitter calibration and turned it off to head out to fly. Out at the field i realized they were mapped wrong again.
I am very familiar with mission planner and am using it correctly. I tried it over usb to eliminate my radios. Dont know if this is causing the issue but I have to run my throttle channel min around 1000 for my castle creation escs to arm. I know now the Rc min max issue has to be fixed before I can remap my extra low throttle pwm min to a different channel. Could the issue I am having be related to the RCn_MIN and RCn_MAX values not being on the correct channel or is this a new issue?