The fare class doesn't have anything to do with your seat location. If booked through AMEX, was it a case of them not selecting a seat at booking? Just check the map constantly. Also make sure that your upgrade is requested, which may not have happened going through AMEX. Is your SkyMiles associated with the reservation and does it show up for you at DL.com? If not, there may be preferred seats available that show up as taken.