### Godot version

4.1 beta 3

The same project works fine on 4.1 **beta 1 and beta 2.**

### System information

Tested on MacOS, Fedora and HTML5

### Issue description

I have a problem in version 4.1 beta 3 with a popup (popup panel). The first time it always displays correctly. Every subsequent time, I only see a black spot. 

[Nagranie ekranu z 2023-06-23 11-35-28.webm](https://github.com/godotengine/godot/assets/5132385/f7a7ad08-754c-4b4b-b594-b6880eff5f3d)

*The same if I show popup by methods like popup_centered.


### Steps to reproduce

I'm trying to reproduce it with a clean and minimal example, but unfortunately, without success. Maybe someone else has this issue or knows a way to reproduce it?

### Minimal reproduction project

I'm trying to create it.
RenderTarget *rt = render_target_owner.get_or_null(p_render_target);
	ERR_FAIL_COND(!rt);
	ERR_FAIL_COND(rt->direct_to_screen);
	if (rt->backbuffer_fbo == 0) {
		_create_render_target_backbuffer(rt);
	}
	Rect2i region;
	if (p_region == Rect2i()) {
		
		glBindFramebuffer(GL_FRAMEBUFFER, rt->backbuffer_fbo);
		glClearColor(p_color.r, p_color.g, p_color.b, p_color.a);
		glClear(GL_COLOR_BUFFER_BIT);
	} else {
		region = Rect2i(Size2i(), rt->size).intersection(p_region);
		if (region.size == Size2i()) {
			return; 
		}
		glBindFramebuffer(GL_FRAMEBUFFER, rt->backbuffer_fbo);
		GLES3::CopyEffects::get_singleton()->set_color(p_color, region);
	}
}
void TextureStorage::render_target_gen_back_buffer_mipmaps(RID p_render_target, const Rect2i &p_region) {