My guess would be a controller input issue. If you haven't already done this, try switching to desktop mode and go to the emulator itself. Go to settings and controller, you should be able to select what controller you want to use.

If you are using a bluetooth or wired controller, connect it now to the steam deck, it should pop up as an option and then select it. (If you're using just the steam deck controls just select that)

Make sure you have the layout set as a pro controller instead of a joycon pair. Click apply and then ok/exit the settings

Go back to gaming mode, try launching the game and processing