### 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.
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_BASE_LEVEL, 0);
	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAX_LEVEL, 1);
	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
	GLES3::Utilities::get_singleton()->texture_allocated_data(rt->sdf_texture_read, rt->process_size.width * rt->process_size.height * 4, "SDF texture (read)");
}
void TextureStorage::_render_target_clear_sdf(RenderTarget *rt) {
	if (rt->sdf_texture_write_fb != 0) {
		GLES3::Utilities::get_singleton()->texture_free_data(rt->sdf_texture_read);
		GLES3::Utilities::get_singleton()->texture_free_data(rt->sdf_texture_write);
		GLES3::Utilities::get_singleton()->texture_free_data(rt->sdf_texture_process[0]);
		GLES3::Utilities::get_singleton()->texture_free_data(rt->sdf_texture_process[1]);
		glDeleteFramebuffers(1, &rt->sdf_texture_write_fb);
		rt->sdf_texture_read = 0;
		rt->sdf_texture_write = 0;
		rt->sdf_texture_process[0] = 0;
		rt->sdf_texture_process[1] = 0;
		rt->sdf_texture_write_fb = 0;
	}
}
GLuint TextureStorage::render_target_get_sdf_framebuffer(RID p_render_target) {
	RenderTarget *rt = render_target_owner.get_or_null(p_render_target);
	ERR_FAIL_COND_V(!rt, 0);
	if (rt->sdf_texture_write_fb == 0) {
		_render_target_allocate_sdf(rt);
	}
	return rt->sdf_texture_write_fb;
}
void TextureStorage::render_target_sdf_process(RID p_render_target) {