With multiple joysticks, game does not correctly remember which buttons are assigned on which joystick
Version 126.96.36.1992 (64 bit, Steam version, no mods)
Windows 7 64-bit
Replicating the problem:
1. You will need two joysticks or joystick-like devices. In my case, I used a Saitek X52 joystick and Saitek rudder pedals, which the system treats the same as a joystick.
2. Ensure both are detected by the game (try to assign buttons or axes in the input settings).
3. Assign a joystick button to a control, e.g. assign a button as the "staging" control.
4. Take note of name of the button which was assigned, e.g. "Joystick1Button1", and verify that it works in game.
5. Restart the game (rebooting the computer is possibly needed to reproduce the problem).
6. At this point, the control will still have the same name in the input settings (i.e. "Joystick1Button1"), but Joystick1 may have become Joystick2, and vice versa, meaning the control settings will no longer work properly in game. You can test to see if the problem has occurred by trying to re-assign the button - if you reassign the button and it detects the button as being on a different joystick (i.e. it was "Joystick1Button1", now it is "Joystick2Button1"), the problem has occurred.
This problem does not seem to happen with joystick axis controls, only buttons. If you assign an axis, then restart, the axis will still be assigned to the correct joystick even if its number has changed. Issue can be game affecting if you do not realise it has occurred until you are already in game.
Manually verify the controls every time you start the game, and reassign them all if necessary.