AX2850 encoder problem

I have an AX2850, and the encoder module is not working. Using Roborun's encoder tab, the counter box remains at 0. Using serial commands ?k and ?K gives the same 0 results. On the encoder port, Pin 2 does not output +5V and Encoder 1 does not register movement. I have verified that there is a 0-5V quadrature pulse train using an oscilloscope.

Verify that the encoder module is detected. In roborun you should see a encoder firmware revision.
If so, then go to the encoder tab and verify that the switch LEDs change as you rotate the shaft after you click on the run button. You should also see the counter values change.
Encoder module failures are very rare, so hopefully it is a simple problem.