I travel on the SYD->SFO route frequently. There can be a delay at gate 53 when all travelers are hand searched, but since they have hired more security staff there have been no queues when I go through.

Is the Qantas flight a domestic or international flight? If it is a domestic flight, it lands at the domestic terminal and there would be a delay while you take a bus to the international terminal.

For a cheaper fare from BNE->SYD for an earlier flight, check out Virgin Blue at www.virginblue.com.au. For some routes I was looking at, it was half the price of Qantas. Of course Virgin Blue flights will be domestic.