my TA mentioned something that may be causing the confusion - she told me that if the flight has no business class cabin they will ISSUE the ticket in Y (or M) but will ENDORSE your ticket to A at the time of booking the specific flight.

This is apparently to prevent you from flying in A class should a particular flight on your sector have a D class cabin. However as far as I know AA doesnt have D except on its Flagship transcons.

So maybe this is where the confusion lies ????