### 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
windows[window_id].minimized = _window_minimize_check(window_id);
			} break;
			case LeaveNotify: {
				DEBUG_LOG_X11("[%u] LeaveNotify window=%lu (%u), mode='%u' \n", frame, event.xcrossing.window, window_id, event.xcrossing.mode);
				if (!mouse_mode_grab) {
					_send_window_event(windows[window_id], WINDOW_EVENT_MOUSE_EXIT);
				}
			} break;
			case EnterNotify: {
				DEBUG_LOG_X11("[%u] EnterNotify window=%lu (%u), mode='%u' \n", frame, event.xcrossing.window, window_id, event.xcrossing.mode);
				if (!mouse_mode_grab) {
					_send_window_event(windows[window_id], WINDOW_EVENT_MOUSE_ENTER);
				}
			} break;
			case FocusIn: {
				DEBUG_LOG_X11("[%u] FocusIn window=%lu (%u), mode='%u' \n", frame, event.xfocus.window, window_id, event.xfocus.mode);
				WindowData &wd = windows[window_id];
				last_focused_window = window_id;
				wd.focused = true;
				if (wd.xic) {
					
					
					MutexLock mutex_lock(events_mutex);
					XSetICFocus(wd.xic);
				}
				
				static unsigned int focus_order = 0;
				wd.focus_order = ++focus_order;
				_send_window_event(wd, WINDOW_EVENT_FOCUS_IN);
				if (mouse_mode_grab) {