### 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
_THREAD_SAFE_METHOD_
	ERR_FAIL_COND_V(!windows.has(p_window), Rect2i());
	const WindowData &wd = windows[p_window];
	return wd.parent_safe_rect;
}
void DisplayServerX11::popup_open(WindowID p_window) {
	_THREAD_SAFE_METHOD_
	WindowData &wd = windows[p_window];
	if (wd.is_popup) {
		
		List<WindowID>::Element *C = nullptr;
		List<WindowID>::Element *E = popup_list.back();
		while (E) {
			if (wd.transient_parent != E->get() || wd.transient_parent == INVALID_WINDOW_ID) {
				C = E;
				E = E->prev();
			} else {
				break;
			}
		}
		if (C) {
			_send_window_event(windows[C->get()], DisplayServerX11::WINDOW_EVENT_CLOSE_REQUEST);
		}
		time_since_popup = OS::get_singleton()->get_ticks_msec();
		popup_list.push_back(p_window);
	}
}
void DisplayServerX11::popup_close(WindowID p_window) {