I don't know. In any case, the idea of backward shield compatibility was a broken one from the outset. Perhaps this is just a quirky consequence of the implementation of what was basically an irredeemably bad idea in the first place.
I agree that the concept of new shield boards being able to coexist nicely with both legacy and new Due boards may have been a bridge too far. While they did define a new shield pin IOREF to give any new shield design using it a hint on what the Vcc voltage of the underlining chip is, I would like to see a schematic of a new shield design that handles bidirectional IO voltage translations. Not saying it can't be done but I suspect from now on most shields will be designed for either Uno or Due only use, but we will see I guess.
IOREF. This pin on the Arduino board provides the voltage reference with which the microcontroller operates. A properly configured shield can read the IOREF pin voltage and select the appropriate power source or enable voltage translators on the outputs for working with the 5V or 3.3V.
Lefty