The delays prior to the QF9, may be attributed to high temperatures in Jo'burg. At 5,500ft elevation, the thrust is significantly reduced and the normal BRW for the service to Sydney is approx 370t. In the summer period, flights often have to wait an extra couple of hours for the temp to reduce to 24 degrees so that they can depart. As this aircraft turns around on arrival in Sydney to operate the QF1 (except Fridays I believe), then this may be the cause of some delays.
I haven't seen any aircraft fitted with premium economy seating yet - they may be doing the Pacific configured aircraft first.