### 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
for (const KeyValue<WindowID, WindowData> &E : windows) {
						if (mouse_mode == MOUSE_MODE_CONFINED) {
							XUndefineCursor(x11_display, E.value.x11_window);
						} else if (mouse_mode == MOUSE_MODE_CAPTURED || mouse_mode == MOUSE_MODE_CONFINED_HIDDEN) { 
							XDefineCursor(x11_display, E.value.x11_window, null_cursor);
						}
						XGrabPointer(
								x11_display, E.value.x11_window, True,
								ButtonPressMask | ButtonReleaseMask | PointerMotionMask,
								GrabModeAsync, GrabModeAsync, E.value.x11_window, None, CurrentTime);
					}
				}
#ifdef TOUCH_ENABLED
				
				/*for (int i = 0; i < xi.touch_devices.size(); ++i) {
					XIGrabDevice(x11_display, xi.touch_devices[i], x11_window, CurrentTime, None, XIGrabModeAsync, XIGrabModeAsync, False, &xi.touch_event_mask);
				}*/
#endif
				if (!app_focused) {
					if (OS::get_singleton()->get_main_loop()) {
						OS::get_singleton()->get_main_loop()->notification(MainLoop::NOTIFICATION_APPLICATION_FOCUS_IN);
					}
					app_focused = true;
				}
			} break;
			case FocusOut: {
				DEBUG_LOG_X11("[%u] FocusOut window=%lu (%u), mode='%u' \n", frame, event.xfocus.window, window_id, event.xfocus.mode);
				WindowData &wd = windows[window_id];
				wd.focused = false;