Perhaps this is the common thread all along?
I, too, received the obnoxious "your application is incomplete" notice from AU, despite the fact that I submitted everything in a timely manner. It was my GRE scores that threw a wrench in the process; there was a communication problem between AU and ETS, which led to my scores not being received promptly by the University. Since this is obviously out of my control, I was informed by AU that I will not be penalized for ETS' tardiness.
So yes, you are not alone, Mal83. And yes, I highly doubt that the last batch are all declines or will receive little to no funding offers. At the end of the day, we have to remind ourselves that we applied to a large institution that receives an enormous load of applications. There is no logic to the insanity of sifting through hundreds of apps, so it is best we throw pessimistic speculation out the window.