Hi,
I have checked and see the flags work. I see that they do not display as they used to. It is because your menu system does not support sub-menu dropdown items.
You can solve that by using [gtranslate] shortcode in menu instead of Show in Menu option.
You can go to Appearance -> Menus -> Custom Link then set URL = # and Link Text = [gtranslate] then Add to Menu.
Thanks! 🙂