The reason your Xbox controller is not working is because it is connecting as controller 2 and will work for 2 player games fine but the menus and such will be searching for controller 1, there is an option in AyaSpace to turn off the built in controller which acts like xbox controller 1 so you can use your own controller paired up to the device as controller 1. Also you may need to go to some games options and enable the controller as this device has a keyboard so defaults to typical mouse and keyboard settings first on some games, it's the games being the issue not the device, so just setting up the controller in the game resolves it, some games are clever enough to use the controller first or have both enabled.
Also depends which service the game was on if on steam you may need to check what steam is doing with the controller as steam has its own controller stuff in the client too, so may need to check there too.
Did you update Ayaspace to version 2.5.0.12 ? The way to check the version is to hold down Ayaspace button get to the main Ayaspace page and click the top left hamburger button, which will show a left side menu with power off at bottom and just above that is the version number you have installed.
If you get double inputs with the external controller for any reason you can go to this option in Ayaspace and turn off this feature too as it is on by default:-
Either that or make sure "desktop layout" is disabled in steam settings to avoid double input.