You guys have been a great help. Now that I think about i MUST have been at the International Terminal Arrivals Area and not a Domestic Terminal.
Reading here:
http://www.ataturkairport.com/mobile...aspx&type=Page
My mistake seems to have been not going to the Transit Desk and having the airline (or most likely a contractor) check my bags thru to BNE on EK (without me actually obtaining the bags). The transfer desk printed my boarding passes so they must have some manual process for collecting the luggage from the separately ticketed VIE to IST leg and then check it in on EK for the rest of my ticket to Australia.