I know you haven't had time to properly test the due with the shield and thus make any changes to your library; so I was hoping to do it for you...
However I've hit a roadblock I can't figure out myself: when trying to upload a sketch that uses the AFMotor library, I get the error: "_B was not declared in this scope". It makes me think that the core Arduino functions are not being loaded properly and I'm guessing it has to do with the following lines of code found in AFMotor.cpp:
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#if (ARDUINO >= 100)
Even if I get rid of the if statement
I still get erros with _BV.
Any quick suggestions?