### 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
_THREAD_SAFE_METHOD_
	Vector<int> ret;
	for (const KeyValue<WindowID, WindowData> &E : windows) {
		ret.push_back(E.key);
	}
	return ret;
}
DisplayServer::WindowID DisplayServerX11::create_sub_window(WindowMode p_mode, VSyncMode p_vsync_mode, uint32_t p_flags, const Rect2i &p_rect) {
	_THREAD_SAFE_METHOD_
	WindowID id = _create_window(p_mode, p_vsync_mode, p_flags, p_rect);
	for (int i = 0; i < WINDOW_FLAG_MAX; i++) {
		if (p_flags & (1 << i)) {
			window_set_flag(WindowFlags(i), true, id);
		}
	}
	return id;
}
void DisplayServerX11::show_window(WindowID p_id) {
	_THREAD_SAFE_METHOD_
	const WindowData &wd = windows[p_id];
	popup_open(p_id);
	DEBUG_LOG_X11("show_window: %lu (%u) \n", wd.x11_window, p_id);
	XMapWindow(x11_display, wd.x11_window);
	XSync(x11_display, False);
	_validate_mode_on_map(p_id);
}
void DisplayServerX11::delete_sub_window(WindowID p_id) {
	_THREAD_SAFE_METHOD_