I'm having a similar situation with my quad.
After lots of experimentation, I was finally able to enable 3 flight modes (Spektrum DX9). I configured the "Gear" switch (Channel 5 on the transmitter) as my arming switch designated as Accessory 0, but every time I change anything from the default values, the vehicle won't arm. I'm not sure what sequence/combination of configuration changes I made to my transmitter and Librepilot, but the RC Input now shows input for 3 flight modes using the transmitter switch D as Accessory 1.
I still can't change anything else without disabling my arming switch.
It's flying just fine with all the default settings.
This AM, I twisted all the motor wires, set the home location, calibrated the magnetometers, connected to 9 satellites, and the GPS and magnetometer alarms show green.
I've tried setting both Stabliized 1 and Stabilized 2 to Velocity Roam, but the arming switch still doesn't arm unless I return all the settings to the defaults.
I must still have some incompatible settings somewhere, but can't figure out where.