Looks like the shader you’re using is a “screen reading shader”. Somewhere in the shader code itself, you’ve got something like hint_screen_texture. Remove that, then a new variable will be exposed in the material variables. Make GodotBoy set it’s texture to that variable.
https://docs.godotengine.org/en/stable/tutorials/shaders/screen-reading_shaders.html
If it works how I think, this texture is taking your entire screen as input. You need to be able to set what exactly it’s catching. Should be easy to fix!
Alternitively, if you wanna learn some shader code, might be good chance to make it read only the part of the screen you want it to. But that might be more effort than it’s worth.
What shader are you using? Looks fun, could be good to include in a future release.