### 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.
int best_idx = -1;
				int best_height = 0x7FFFFFFF;
				for (int j = 0; j <= base_size - si.size.width; j++) {
					int height = 0;
					for (int k = 0; k < si.size.width; k++) {
						int h = v_offsets[k + j];
						if (h > height) {
							height = h;
							if (height > best_height) {
								break; 
							}
						}
					}
					if (height < best_height) {
						best_height = height;
						best_idx = j;
					}
				}
				
				for (int k = 0; k < si.size.width; k++) {
					v_offsets[k + best_idx] = best_height + si.size.height;
				}
				si.pos.x = best_idx;
				si.pos.y = best_height;
				if (si.pos.y + si.size.height > max_height) {
					max_height = si.pos.y + si.size.height;
				}
			}
			if (max_height <= base_size * 2) {
				atlas_height = max_height;