Anyone got this encoder library to work with the due?

http://www.pjrc.com/teensy/td_libs_Encoder.html

Doesn't seem to count any pulses on my side, works with the UNO tho.

By the way, the voltage output of the encoder is about 40 mV for a high when Vcc is connect to 5V, is that normal?

40mV is decidedly LOW. Do you have a pullup? Internal pullups are usually sufficient.

MorganS:
40mV is decidedly LOW. Do you have a pullup? Internal pullups are usually sufficient.

Hmmm that seemed to work after I added write high to my pins in setup. Odd since I didn't have to do that on the Uno