We have seen many reports of this on this site. Unfortunately, none of the Laminar Research employees have been able to recreate the issue to track down the specific bug. We've tried CH Products yoke & rudder pedals, Saitek equipment, and a Thrustmaster joystick, among other products.
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 have additional aircraft/plugins/scenery, etc, and would like to help us see if something is interfering, 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.