The same thing happened to me. I booked some travel on NW and both of the flights looked completely full when looking at the seat map. When I checked in online though there were quite a few open seats and the online check in let me pick any seat on the plane. My connection in MEM to IAH was showing full on the seat map too but the plane was near half empty when I got on. Who knows why all the seats are blocked off? I would check in early online. If that doesnt work show up early at the airport and talk with the GA they are usually happy to help