We were not able to reproduce this behavior. We have heard some people are having problems using the controllers if they were off when the sim was started, and later turned on, so make sure you turn everything on before starting X-Plane.
Make sure everything is updated (SteamVR, anything from the set manufacturer, etc). Try resetting to default preferences to see if that helps:
Move the preferences folder (found in the Output folder) to the desktop, then restart X‑Plane and default preferences will be restored. If the default preferences do not fix your problem, you can simply replace them with the folder you moved to the desktop and restore your personalized settings.