I had the same thing happen to me. I booked a DCA-JFK-GIG ticket using BA Avios and changed the FFN to my AA number. I called the EXP line, and the agent said that because it was a mileage ticket, I wouldn't be able to get the seat assignments that I would normally get as an EXP. This made no sense, so I sent a direct message to the AA Twitter team. They were able to assign me the seats I wanted without any issues. Interestingly, I'm not allowed to change my seats when I log into the booking, but the MCE seats I requested through Twitter are there.