### 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 (window_id_other != INVALID_WINDOW_ID) {
						int x, y;
						Window child;
						XTranslateCoordinates(x11_display, wd.x11_window, wd_other_x11_window, event.xbutton.x, event.xbutton.y, &x, &y, &child);
						mb->set_window_id(window_id_other);
						mb->set_position(Vector2(x, y));
						mb->set_global_position(mb->get_position());
					}
				}
				Input::get_singleton()->parse_input_event(mb);
			} break;
			case MotionNotify: {
				
				
				
				WindowID focused_window_id = _get_focused_window_or_popup();
				if (!windows.has(focused_window_id)) {
					focused_window_id = MAIN_WINDOW_ID;
				}
				while (true) {
					if (mouse_mode == MOUSE_MODE_CAPTURED && event.xmotion.x == windows[focused_window_id].size.width / 2 && event.xmotion.y == windows[focused_window_id].size.height / 2) {
						
						center = Vector2(event.xmotion.x, event.xmotion.y);
						break;
					}
					if (event_index + 1 < events.size()) {
						const XEvent &next_event = events[event_index + 1];
						if (next_event.type == MotionNotify) {