Hi Ellieb,
I could use some more information about your set up--what OS, etc.
We have been seeing a lot of issues on this forum about issues with El Capitan, X-Plane, and USB devices. Such as: devices are recognized by OSX itself but not in X-Plane, there is no response and in the calibration menu no movement of all axis. Unplug/plug in all devices and re-calibrate them. This seems to be working so far, although I'm sure it is annoying if you fly a lot.
I have also heard that if there is a device control manager it can also cause problems. If you can provide your system information and specific steps of what you have tried and the results, we can continue to trouble shoot this bug.