### 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.
Texture *texture = texture_owner.get_or_null(p_texture);
	ERR_FAIL_COND(!texture);
	glActiveTexture(GL_TEXTURE0 + p_texture_no);
	glBindTexture(texture->target, texture->tex_id);
}
void TextureStorage::texture_add_to_texture_atlas(RID p_texture) {
	if (!texture_atlas.textures.has(p_texture)) {
		TextureAtlas::Texture t;
		t.users = 1;
		texture_atlas.textures[p_texture] = t;
		texture_atlas.dirty = true;
	} else {
		TextureAtlas::Texture *t = texture_atlas.textures.getptr(p_texture);
		t->users++;
	}
}
void TextureStorage::texture_remove_from_texture_atlas(RID p_texture) {
	TextureAtlas::Texture *t = texture_atlas.textures.getptr(p_texture);
	ERR_FAIL_COND(!t);
	t->users--;
	if (t->users == 0) {
		texture_atlas.textures.erase(p_texture);
		
	}
}
void TextureStorage::texture_atlas_mark_dirty_on_texture(RID p_texture) {