A couple of things. Firstly, Fair Trading are notoriously unreliable and it’s pot luck whether you get someone who knows and cares about strata or someone who is as dim and uninformed as the person you spoke to.
Secondly, just because the law says you are entitled to something, doesn’t mean you don’t have to fight for it. If you have lodged your claim within the statutory window, then it is a valid claim, regardless of what the airhead at Fair Trading said.
Finally, Fair Trading can’t issue rulings on anything. They are there to advise and mediate. They will try to get parties to agree but in an ongoing dispute, any independent rulings have to be made by NCAT.
Finally, if it’s any consolation, I’m guessing that you were always going to have to take this builder to NCAT anyway, especially when they are playing fast and loose with the facts.
Start the process by asking for mediation, get all your facts and figures lined up, and go in with the attitude that you are all set to go to NCAT if you don’t get everything you feel you are entitled to. Keep emotion out of it but stay strong.