### 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
ERR_FAIL_COND_V(!windows.has(p_window), ObjectID());
	const WindowData &wd = windows[p_window];
	return wd.instance_id;
}
DisplayServerX11::WindowID DisplayServerX11::get_window_at_screen_position(const Point2i &p_position) const {
	WindowID found_window = INVALID_WINDOW_ID;
	WindowID parent_window = INVALID_WINDOW_ID;
	unsigned int focus_order = 0;
	for (const KeyValue<WindowID, WindowData> &E : windows) {
		const WindowData &wd = E.value;
		
		if (wd.focus_order == 0) {
			continue;
		}
		
		WindowID window_id = E.key;
		Rect2i win_rect = Rect2i(window_get_position(window_id), window_get_size(window_id));
		if (win_rect.has_point(p_position)) {
			
			if ((parent_window != wd.transient_parent) || (wd.focus_order > focus_order)) {
				found_window = window_id;
				parent_window = wd.transient_parent;
				focus_order = wd.focus_order;
			}
		}
	}
	return found_window;
}
void DisplayServerX11::window_set_title(const String &p_title, WindowID p_window) {