Mind you, there are many fare buckets on one single flight - it can range from 60 bucks to 150 bucks between SYD and BNE on the same flight for example.
Once a lower fare bucket is emptied (sold out) the system bumps you to a higher fare bucket.
Moreover, (I learned this afterward), many times they only release 1 seat at a time at the cheapest fare bucket - so if you book 2, you are immediately bumped to a higher bucket. What you can do is, buy 1 ticket at the cheapest fare on that flight, and then see if a second seat is released at that fare. Or just buy 1 cheapest and buy 1 the second cheapest.
The fare differences on Qantas Red Tail can be $40 Aus Dollar between each bucket the time we went.
Needless to say, during price war between Virgin Blue and Qantas, one can find SYD/BNE at $46. Unbelievable.