When you are booked on a 'backup' flight .. the question to ask the Ticket/Gate agent is 'Did you put the arunk in the proper place?'
While not an expert of the details of arunk, I understand it stands for 'arrival unknown'. I am not sure it goes between the two outbound reservations or before the next reservation.
It is designed to do prevent exactly what happened to you. AAA-BBB with a backup or AAA-XXX-BBB then returning BBB-AAA later. If the computer thinks you no-showed on the outbound (or middle) legs, all subsequent reservations get cancelled (DID WE TELL PEOPLE ABOUT THIS WHEN ASKED ABOUT THROW-AWAY CITIES ON AN OUTBOUND??).
Compensation . no $$ .. and in my opinion no miles. The AAgent got you to the destination.
You found out about this while on the cruise that AA did not have your reservation onboard and luggage tags. I would not have wasted the phone calls from onboard (even with signal) and just headed to the airport to take care of this when you finished the cruise. The AA people onboard could not help you as they have no computers only boarding passes and luggage tags....very typical setup.
Next time .. be smart and ask the arunk question and they will know why you fly!