An update, after I checked with QF and they again confirmed it was ok, the TA still was saying it couldn't be done because of passing through BNE twice (I felt this was a misunderstanding of the "can't cross point of origin" rule).
I persisted and asked them to specifically check with QF in light of the rules.
By this stage I was starting to feel that the TA was getting her back up at my persistance, and was seriously thinking of starting over again with QF or AA directly, but for the fact that the flights I had spent time finding were held under the TA's PNRs and would have to be cancelled and started over again.
Eventually, I got a message back saying that Qantas had agreed to "waiver the rules" and book it

So, the moral of the story for me: Next time will book with AA!

But now I have that contented feeling that comes once an itinerary is finalised, and just the travel to look forward to!