Why was your itinerary noted with your QF number on it anyway? ON AA flights, it could be segment selected... ie certain flights go to certain FF number etc.. This also works up to a point with CX as long as its not connecting flights on the same day.

QF and BA have different systems altogether in that it just remembers the first FF number placed there.

Try and speak to someone at QF FF Club about it. This can be done. I've had situations about a few years back when a flight mileage accidentally went into BA when I wanted it on QF. Well, BA had to issue a letter, and it did. So QF should do likewise. Or else, what you can try to do is to fax MPC a copy of your statement during which you took the respective flights which did not show up on yoru statement.

Please note too that only certain booking codes allow mileage credit. QF and CX have different codes by AA for their programmes.

Check again.