I've just wasted a bunch of time booking return flights from BNE to SYD. I always used iwantthatflight (who have a rep here) because they search across many discount travel agents and have always showed the final price. But some of the agents that they refer to are really dodgy - blatant bait and switch manoeuvres.
I tried SEVEN times to book a flight from SYD to BNE. Each time, the price would show up and I'd select it to book, I'd be redirected to the agents site and fill in the details and payment, then when I tried to book one of two things would happen:
The flight would suddenly be booked out. I would then be redirected to a the agents search page to select a different flight, but it would still show the same cheap flight that I tried to book.
I would receive a notice to say that the price had increased while I was booking - and by the seventh time I was getting pretty quick at filling in the form - it's not like I left it open for 30 minutes. Normally this price increase would be about 40%. Once, it was about 15%, so I resigned to just paying it and clicked the agree button, then it told me there had been another price increase of another ~20% percent. Of course, when I went back to the search function it would bring up the lower priced flight again.
I could try reporting this to the ACCC, but we all know how much that will do. I have reported it to iwantthatflight so that maybe they'll stop searching/indexing the offending agents.
That sounds like a massive price hike in a short period of time. Usually one of the reasons why flight prices go up is if you have left your cookies on so the travel agents know you want that flight so each time you search for it they gradually increase the price. So it may be worth turning your cookies off or just use a different browser to search (eg. mozilla) and one to actually book your flight (eg. chrome)
I book flights quite regularly and have found www.kayak.com and www.skyscanner.net to be the most reliable