Like ostsjoe said, you probably need to reorder your controllers and set the deck to be controller 1. You can do this in two places:
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Open the QAM menu (the ". . ." button), open the gear tab, and there should be a "reorder controllers" button. This button only appears if additional controllers are connected, or if the Deck is currently set to a controller slot other than 1.
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Press the steam button, and open the controller configuration menu for the game. At the top there should be a button to reorder the controllers.
Rarely I've also had where a game identified a controller in spot 2/etc as the one I was playing with, and the deck had to be set to that controller slot for the game to work until I relaunched the game.