### Godot version

Master (0ddd9c3e8f9088fa139e25b2903289d727073e12)

### System information

PopOS 22.04 - Intel integrated graphics - all backends

### Issue description

When there are popup windows in the editor, I cannot click on the "Confirm"/"Cancel" type buttons at the button. 

I have the issue both in the project manager (importing projects I can click on files etc. but cannot click "open") and when running the editor (cannot click "Save&Quit" etc.)

Sometimes the editor correctly highlights the buttons and I can use the arrow keys to navigate the buttons and "enter" to confirm my selection.

_I can navigate the editor closing dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-24-06](https://user-images.githubusercontent.com/16521339/212774269-d784ea5e-5921-4460-9124-48978939c8e7.png)

_I can't navigate the project import dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-29-00](https://user-images.githubusercontent.com/16521339/212774683-0a80795a-eed4-4e65-b2ca-3562c25d71fd.png)


### Steps to reproduce

Run the editor

### Minimal reproduction project

Reproducible in the project manager
if (((mask & Button1Mask) || (mask & Button2Mask) || (mask & Button3Mask) || (mask & Button4Mask) || (mask & Button5Mask))) {
					List<WindowID>::Element *C = nullptr;
					List<WindowID>::Element *E = popup_list.back();
					
					while (E) {
						
						Rect2i win_rect = Rect2i(window_get_position(E->get()), window_get_size(E->get()));
						
						Rect2i safe_rect = window_get_popup_safe_rect(E->get());
						if (win_rect.has_point(pos)) {
							break;
						} else if (safe_rect != Rect2i() && safe_rect.has_point(pos)) {
							break;
						} else {
							C = E;
							E = E->prev();
						}
					}
					if (C) {
						_send_window_event(windows[C->get()], DisplayServerX11::WINDOW_EVENT_CLOSE_REQUEST);
						closed = true;
					}
				}
			}
			last_mouse_monitor_mask = mask;
		}
	}
	return closed;
}
void DisplayServerX11::process_events() {