On board controller works as expected unless you attach a Bluetooth controller it seems. I need to reboot the deck for them to work again.
Yeah, I remember having the same issues with external controllers. And our players reported them too.
But today I tested our game with PS4 bluetooth controller and it works perfectly fine on Steam Deck. I tried switching back to Steam Deck controller and it too works fine, I didn't even have to disconnect the PS4 one. I don't know what has changed...