### 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 (wd_other.focused) {
							int x, y;
							Window child;
							XTranslateCoordinates(x11_display, wd.x11_window, wd_other.x11_window, event.xmotion.x, event.xmotion.y, &x, &y, &child);
							Point2i pos_focused(x, y);
							mm->set_window_id(E.key);
							mm->set_position(pos_focused);
							mm->set_global_position(pos_focused);
							mm->set_velocity(Input::get_singleton()->get_last_mouse_velocity());
							Input::get_singleton()->parse_input_event(mm);
							break;
						}
					}
				}
			} break;
			case KeyPress:
			case KeyRelease: {
#ifdef DISPLAY_SERVER_X11_DEBUG_LOGS_ENABLED
				if (event.type == KeyPress) {
					DEBUG_LOG_X11("[%u] KeyPress window=%lu (%u), keycode=%u, time=%lu \n", frame, event.xkey.window, window_id, event.xkey.keycode, event.xkey.time);
				} else {
					DEBUG_LOG_X11("[%u] KeyRelease window=%lu (%u), keycode=%u, time=%lu \n", frame, event.xkey.window, window_id, event.xkey.keycode, event.xkey.time);
				}
#endif
				last_timestamp = event.xkey.time;
				
				
				_handle_key_event(window_id, &event.xkey, events, event_index);
			} break;
			case SelectionNotify: