I just had an issue using sbus, but it wasn’t recognizing rc channels 9+. See my post here.
Maybe try running the update commands staroselskiy mentioned. Also maybe try these commands mentioned when you think the receiver is not working. Seems like you could narrow down if it is software or hardware issue.
What caught my interestin your post was that while troubleshooting no rc ch9+ pwm I was changing modes on my receiver (futaba 7008sb needs to be on mode 2 to output sbus… maybe your receivers need the same configuration??) and it was easier to power cycle the receiver by unplugging the cable going into sbus rather than powering down the whole system. When I did this I had the same results you are now. Receiver showed connected to the transmitter but navio2 didn’t see any pwm input. I would restart and try again but it was intermittent. Because I was still troubleshooting I said screw it and reflashed and built the experimental branch using waf and all seems to be working. Haven’t flown yet but have tested all rc channels and powered the motors up.
Oh and I am also using rpi3 with navio2 and the latest rt kernel image.