### 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_V(!rt, RS::VIEWPORT_MSAA_DISABLED);
	return rt->msaa;
}
void TextureStorage::render_target_request_clear(RID p_render_target, const Color &p_clear_color) {
	RenderTarget *rt = render_target_owner.get_or_null(p_render_target);
	ERR_FAIL_COND(!rt);
	rt->clear_requested = true;
	rt->clear_color = p_clear_color;
}
bool TextureStorage::render_target_is_clear_requested(RID p_render_target) {
	RenderTarget *rt = render_target_owner.get_or_null(p_render_target);
	ERR_FAIL_COND_V(!rt, false);
	return rt->clear_requested;
}
Color TextureStorage::render_target_get_clear_request_color(RID p_render_target) {
	RenderTarget *rt = render_target_owner.get_or_null(p_render_target);
	ERR_FAIL_COND_V(!rt, Color());
	return rt->clear_color;
}
void TextureStorage::render_target_disable_clear_request(RID p_render_target) {