Unfortunately, between the Laminar Research employees, we have not yet been able to recreate any issues with X-Plane 10, El Capitan, and flight hardware. We've tried CH Products yoke & rudder pedals, Saitek equipment, and a Thrustmaster joystick.
I have not seen your log.txt to see if you have a lot of third party addons installed. Plugins can interfere in all sorts of ways. If you do have a lot of additional aircraft/plugins/scenery, etc, you can try to determine if one of them is the problem by moving those folders to the desktop. You can also try divide and conquer to narrow down the specific item: remove half and see if the problem persists. Keep removing a chunk of add ons at a time until you find the problem.