I'm having a similar problem except I can see my stick movements on the HITL and Remote control imput. Arming is set to yaw left.
I just did a mod on my drone which included soldering the cc3d wires on the receiver. When I did that I mixed up a few signal wires but I understand that the cc3d picks that up and fixes it (I think). my problem is that even though the cc3d picks up the stick movements and is set to arm, it doesn't.
All help is appreciated.