This has always been one of my biggest disappointments with aa.com. I am getting sick and tired of calling after I make a reservation. I ask to put in my QF number. The other problem is that if you check-in online or at the kiosk the boarding pass can only show an AA FF#, so even if I have called to add my QF# the online boarding pass shows nothing, which makes it a hassle if I don't get credit, so I have to stand in line to get a "real" boarding pass at check-in.
On another note, AA is using O class more and more for domestic US internet fares, which is not listed as earning anything on CX. Has anyone had any luck in crediting an O fare to CX??