Do you have Send F11 in your running script? Because i've been trying to get Citra to launch fullscreen but it was only doing it every other time. The F11 was turning fullscreen on when i exited and then off again the next time i exited.
They have a mode switch for the joysticks, add a button or jump it with a screwdriver, see if that helps
https://forums.cdn.launchbox.gg/monthly_2025_05/71CW7oJxhhL._SL1491_.thumb.jpg.2d8406720759410ee8709e9f8b5c2658.jpg