Did you build your Recalbox yourself, or did you buy everything ready, or did you download a ready image from the internet?
Did the Joystick never work in Recalbox, or did it, and stopped working?
Have you ever tried to remap the controller on the Emulationstation?
Every games are working when my Gamepad is unplugged.
Did you do this test using a keyboard, or, another joystick?
If the joystick never worked, and it works without it, it may be incompatible drivers, and if so, there is no solution.