I did.
This took a few hours to figure out, but I couldn't leave it on a sour note, that would be unfair.
I took the stick off and unplugged it, running just the VPForce, rudder and throttle quadrant, and it all worked again.
So that left the stick, I changed the Warthog stick from VKB adapter to stock Thrustmaster Warthog, and plugged it in it worked, all inputs worked, game works.
Now I finished a round of testing after changed it back to VKB adapter with Rhino Adapter, which again didn't work, then back to Thrustmaster which works, so the issue appears to be the adapter between the Rhino and the VKB.