When I get to joystick calibration, there is no little square visible, but the co-ordinates at the bottom of the screen do respond to my joystick. However, when I push a button, the calibration just ends without asking me to position the stick to the top-left or bottom right. This feels like the same result as you would get by hitting a keyboard button to skip the calibration.

If I then ignore that the calibration failed and jump into the game, the buttons on the joystick work but the axis does not. Even if I map the trigger to joystick button 0, the gun fires, which leads me to believe that the game is picking up joystick button presses.

The most frustrating part is that although I encountered this issue to begin with, something must have fixed it and I had everything almost working. I was in the process of mapping buttons and doing a few more tweaks to get the hat working whilst following Phil's guide when it broke again.

I have these settings:

joysticktype=fcs
timed=true
autofire=false
swap34=false
buttonwrap=true

The control is also set to thrustmaster in-game. I tried timed=false, but that caused the joystick to drift when it was working and is changing nothing with the calibration problem now.

Another problem I already had but fixed (somewhat) is that my keyboard was interfering with the joystick. My workaround is to unplug the keyboard whenever I start up WC. I have also ensured that there are no other USB controllers connected.

Anyone have any idea what might be causing this? It seems like the joystick is working; the game just doesn't want to calibrate it for some reason.

It was the mapper. I deleted the mapper file and calibration started working again.