@Paddy Hi Paddy,
you have to connected your receiver signal (DSM, SBUS or PPM) to connector E4 pin 4 when using ArduPilot (connect receiver GND to BeagleBone Blue GND as well), the DSM2 connector does not work here. Do you have a scope to check the signal voltage? If not, you may have a Arduino (5V) and can use this project https://github.com/mirkix/ardulevel that show the signal level. At some OrangeRX the signal is 3.3V even it is powered by 5V.
Regards
Mirko