Lufthansa has a flight from SFO to FRA normally departing around 2:20PM. I'm not sure how many hours prior to flight the check in opens. Maybe 3? Just guessing, but I don't think they staff these desks 24H. If that is the case, then I think you would not be able to check in for the MUC flight until 10AM or 11AM - whenever the check in desks are staffed.