I suspect your original reservation was booked with AA using AA flight number and AAdvantage number. This has happened to me a few times. It seems to me that QF computer only passes the flight info to AA as it was booked under AA flight number; it is the AA computer which process the credit using whatever number was entered on their end.

You would need to call AA to change your FFP prior to flight. I don't know if you could reverse it now. It didn't matter much to me at the time. Also note that QF flight with QF code shows up in QF account within hours, while QF flight with AA code would show up after about one week. My guess is that the flight info gets passed to AA computer, than passed back to QF computer, if booked with QF FFP. Funny the way it works.