The Due's SAM3X8E has a build in quadrature docoder logic (build into the Timer/Counter)
I'm trying to get it running on the Due http://arduino.cc/forum/index.php/topic,140205.0.html
I'll post any progress in that topic
no progress till now, sorry
I had some exams the last weeks. Maybe I'll have time to work on it next week. I'm still stuck on configuring the Timer/Counter and how to use the routines provided by the ASF-Package. Any help is welcome