After connecting my Switch Pro controller with Toshiba stack and WiinUPro 0.9.2, some games (e.g. Cuphead) will add a second player after pressing a button. The controller is set as X-input and I'm not sure how to fix this issue.
Sounds like for those games you don't need to use WiinUPro if you don't want to. The game is seeing both the Pro Controller itself as a Direct Input device that is created when connecting the controller to Windows and then it also sees the XInput device created via WiinUPro.
It seems Windows no longer allows the option to give a single program exclusive access to a device (unless its the camera).