Morning mate, I took your advice and phoned up and we found what the issue was...
On the morning of the 28th when I received DSC confirmation email from Qantas, I asked our booking department to go ahead and book all my required flights until the end of the year.
My flights were booked via our Amex Concur account at 9:30am eastern time, however the system works, it has thrown my booking times back into Zulu time placing the booking times in the system as just before midnight on the 27th!
So the system is showing 12 of my flights being booked the day before (11pm Zulu), but after opening up the itinerary, it shoes the Australian booking time as the morning of the 28th.
Unfortunately Qantas can't do anything at this point and have said I will need to wait the 8 weeks for each itinerary and then call up to try and have the SC manually added is it's handled by a separate department.
Just some good old fashioned bad luck with the system we use booking in another timezone along with our booking girls being a little too effecient lol.
Will have to see how I got in a few months at claiming these credits.