Did you happen to find a solution to this? I'm having the same problem.
Because of other projects, I have stepped away from my 3DR Quadcopter with the Pixhawk.
From memory, I think I went back to the drawing board, re-flashed the firmware, and did a complete setup from the beginning in Mission Planner.
Then it all worked. Sorry I can't be more specific. For my applications, my APM and Pixhawk are now obsolete.
I am also facing the same problem. Mission planner shows "No RC Receiver" while the same receiver was working with similar connections with Pixhawk 2 days earlier. Please someone guide!!! Thanks