### 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.
if (rt->direct_to_screen) {
		return;
	}
	
	for (KeyValue<uint32_t, RenderTarget::RTOverridden::FBOCacheEntry> &E : rt->overridden.fbo_cache) {
		glDeleteTextures(E.value.allocated_textures.size(), E.value.allocated_textures.ptr());
		
		if (E.value.fbo != rt->fbo) {
			glDeleteFramebuffers(1, &E.value.fbo);
		}
	}
	rt->overridden.fbo_cache.clear();
	if (rt->fbo) {
		glDeleteFramebuffers(1, &rt->fbo);
		rt->fbo = 0;
	}
	if (rt->overridden.color.is_null()) {
		if (rt->texture.is_valid()) {
			Texture *tex = get_texture(rt->texture);
			tex->alloc_height = 0;
			tex->alloc_width = 0;
			tex->width = 0;
			tex->height = 0;
			tex->active = false;
			tex->render_target = nullptr;
			tex->is_render_target = false;
		}
	} else {