Forget it. I was being a dope. The chip I'm trying to interface with was designed for CMOS 5V logic and has a minimum voltage spec on its pins of 4V. When powered by the pins themselves it can see the signaling. As soon as it as it's own 12V supply from Vin, game over with the 3.3V logic.
I'm having to integrate one of these:
TXB0108 to run the conversion. Sweet chip, does automatic direction detection. Breadboard prototyping unit available here:http://www.adafruit.com/products/395
In case anyone else finds themselves having to interface the Due with 5V modules and/or chips.