### 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.
Ref<Image> image = Image::create_empty(4, 4, false, Image::FORMAT_RGBA8);
	image->fill(Color(1, 0, 1, 1));
	Vector<Ref<Image>> images;
	if (p_layered_type == RS::TEXTURE_LAYERED_2D_ARRAY) {
		images.push_back(image);
	} else {
		
		for (int i = 0; i < 6; i++) {
			images.push_back(image);
		}
	}
	texture_2d_layered_initialize(p_texture, images, p_layered_type);
}
void TextureStorage::texture_3d_placeholder_initialize(RID p_texture) {
	
	
	Ref<Image> image = Image::create_empty(4, 4, false, Image::FORMAT_RGBA8);
	image->fill(Color(1, 0, 1, 1));
	Vector<Ref<Image>> images;
	
	for (int i = 0; i < 4; i++) {
		images.push_back(image);
	}
	texture_3d_initialize(p_texture, Image::FORMAT_RGBA8, 4, 4, 4, false, images);
}
Ref<Image> TextureStorage::texture_2d_get(RID p_texture) const {