Hey,
A friend of mine has been having issues with the controller, playing on Steam on Windows. Often the game does not seem to recognise the controller, and a ritual of turning Steam Input on and off and sometimes on again is the only thing that seems to make it work again (everything works smoothly with other games). Sometimes two controllers are connected, but only one is recognised until the same ritual is performed. This also tends to mess up the custom button configurations.
Any ideas on how to fix this?