I also had a weird experience after having a DONE4 re-issued in SYD. It was originally hand-written by Emeco in CAI and then re-issued by the AA ticket office in N. Sydney.

My next onward segment was an open QF segment SYD-AKL. I confirmed a date/time directly with QF. At check-in, my AAdvantage # appeared on the boarding card but the flight did not get credited to my account. Every other segment on the entire itinerary was properly credited.

I am guessing that the reason the flight did not get credited was because it was never booked in AA's res system but that should not make a difference. Or should it?