This site is being deprecated.
Please see the official X‑Plane Support page for help.
Using the control manager software from the hardware manufacturer means X-Plane will not try to help configure your devices. If you uninstall the software, does it fix the issue?
If the software is preventing you from assigning buttons, you can file a bug report with as much info and steps as possible, because the joystick should still work and be configurable with the software, you just have to set it all manually.
This site is no longer being actively maintained.