It was then that they realised my account had been hacked.
I think you are looking in the wrong place.
Its important to note here, that your account has not been 'hacked'. By definition that means someone has broken into a computer and got into your account by a backdoor. If Qantas was hacked, then it would be all over the news. If it was your computer was hacked, or only your account at Qantas that was hacked, have a think for a second, what made you so special to be targeted?
The most likely scenario is your password was compromised, and from the story you tell it does seem like they began by accessing your email account first. as you mentioned, they changed your Qantas password, they didnt know it first, Then how else would they be able to to go through the forgot password your password after you changed it without having access to your email!
Some people like to use the same password for everything. Its not a bad idea for some random chat forum online, but not the same as your email. Its very common for rogue websites to test the passwords clients have used against the email address provided and then go postal with the information they can find in your email account. Services, paypal accounts, frequent fliers. With access to an emaiil account, they can do anything, and take over everything. And you wont even know as they delete all the emails in/out before you see them.
If I was you, even if what I said doesnt sound right, is change ALL your passwords for all Email accounts immediately. And never use the the password with your email address with ANYTHING else at all. Set up whatever secondary authentication they offer, with Gmail there is a code texted to your phone if you sign in on a different computer. Then do the same with anything that is really Yours, like Facebook, Ebay, banks.
Personally, this doesnt sound like any security breach on your computer based on the info given.