Hello, guys!
Could you please post the output of cat /sys/kernel/rcio/rcin/ch2 and move throttle stick up and down to make sure RCIO processes data? And also Could you please post the output of sudo update-alternatives --display arducopter? We need to verify that navio2 binary is selected.
It should be something like this in case of a quadcopter:
Mind the navio2 in the link!