Oddly enough, mine did - and even better, they posted as J - with a class Bonus (And it was on SYD-LAX and MEL-PER too ^ )

I recently did the AAPlat challenge, and had a booking with both QFF and AA numbers in the booking, thanks to my travel agent.

Every flight boarding pass printed with the QFF number - But all checkin staff were happy to change the number to AA and all flights posted correctly and automatically.

So, I think the key is to check it AT CHECKIN and get it changed - Even if it doesn't post automatically, it should be easy to get it posted if your AA number is on it.

I changed the FF number after my SYD-LAX upgrade had been processed, and my MEL-PER was an ODU at the QP - Which they were happy to process even though my BP had an AA number on it. (Using my QFF number obviously)

Chrisb.