### 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.
ERR_FAIL_COND(rt->sdf_texture_write_fb != 0);
	Size2i size = _render_target_get_sdf_rect(rt).size;
	glGenTextures(1, &rt->sdf_texture_write);
	glActiveTexture(GL_TEXTURE0);
	glBindTexture(GL_TEXTURE_2D, rt->sdf_texture_write);
	glTexImage2D(GL_TEXTURE_2D, 0, GL_R8, size.width, size.height, 0, GL_RED, GL_UNSIGNED_BYTE, nullptr);
	GLES3::Utilities::get_singleton()->texture_allocated_data(rt->sdf_texture_write, size.width * size.height, "SDF texture");
	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_NEAREST);
	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_NEAREST);
	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);
	glGenFramebuffers(1, &rt->sdf_texture_write_fb);
	glBindFramebuffer(GL_FRAMEBUFFER, rt->sdf_texture_write_fb);
	glFramebufferTexture2D(GL_FRAMEBUFFER, GL_COLOR_ATTACHMENT0, GL_TEXTURE_2D, rt->sdf_texture_write, 0);
	int scale;
	switch (rt->sdf_scale) {
		case RS::VIEWPORT_SDF_SCALE_100_PERCENT: {
			scale = 100;
		} break;
		case RS::VIEWPORT_SDF_SCALE_50_PERCENT: {
			scale = 50;
		} break;
		case RS::VIEWPORT_SDF_SCALE_25_PERCENT: {
			scale = 25;
		} break;