After getting the right image and binary loaded I was able to get through the Accel and Compass calibration in QGroundControl fairly easily (weird issue on recalibration of the Compass if anyone is interested but worked around it by unchecked the second compass).
I am now trying to do RC calibration using mode 2 and I get to the point where it is trying to read the max right and left of my roll/pitch stick (using the Turnigy IGY-i6 as has been recommended in other threads) and roll values do not register. If I go up when asked to go right and down when asked to go left those values get read but then I'm stuck as nothing else takes.
I tried again with APM Planner as well and noted that when I moved the roll left and right the values did not register there as well. I'm using the jdrones ppm encoder as recommended on ardupilot and by @imuguruza on another thread (PPM Encoder v2.0, Copter) connected to the pwm rail as per documentation and as noted all other values (throttle, yaw, pitch) all get read without issue.
Any thoughts on what might be wrong would be appreciated? I can take a video of what is occurring if that would help as well.
Setup: PXFMini/RPi3 running the Framebuesa Erle-Brain3 image and hexa binary installed