I'll try my best to guide you. You can try moving your Preferences folder "..\X-Plane 11\Output\preferences" out of x-plane's folder. Somewhere you can remember (like your desktop). This you do with the SIM closed. After you moved that folder you run it again, all your settings will be gone, but that way you can test your joystick from scratch. If this fix the problem you just need to set all your keys and axis again. If not...well we'll have to find out what's wrong.
PS: Sorry for my bad English, it isn't my main language.!