### 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 (delta > 250) {
				
				if (OS::get_singleton()->get_main_loop()) {
					DEBUG_LOG_X11("All focus lost, triggering NOTIFICATION_APPLICATION_FOCUS_OUT\n");
					OS::get_singleton()->get_main_loop()->notification(MainLoop::NOTIFICATION_APPLICATION_FOCUS_OUT);
				}
				app_focused = false;
			}
		} else {
			time_since_no_focus = OS::get_singleton()->get_ticks_msec();
		}
	}
	do_mouse_warp = false;
	
	bool mouse_mode_grab = mouse_mode == MOUSE_MODE_CAPTURED || mouse_mode == MOUSE_MODE_CONFINED || mouse_mode == MOUSE_MODE_CONFINED_HIDDEN;
	xi.pressure = 0;
	xi.tilt = Vector2();
	xi.pressure_supported = false;
	LocalVector<XEvent> events;
	{
		
		MutexLock mutex_lock(events_mutex);
		events = polled_events;
		polled_events.clear();
		
		_check_pending_events(events);
	}
	for (uint32_t event_index = 0; event_index < events.size(); ++event_index) {
		XEvent &event = events[event_index];
		if (ignore_events) {