How long was your connection in JFK? Usually when a carrier un-assigns your seats they are most of the way through the process of removing you from the flight and auto-cancelling your trip — glad you made the flight!

Sorry to hear that AA was unable to check you in at BOS for both sectors. That sounds like a failure on their part. There is not a lot you could have done differently, except possibly trying to check in online for your airberlin flight as soon as your BOS-JFK had taken off.