BasicMicro

1. If you have a scope, check the encoder signal lines. They should be clean square waves when running the motor at a constant velocity. If you dont have a scope you can manually check the encoder signal states with a multimeter. Just move the motor a little till you see 0v and then 5v

2. Assuming that works, uncheck the swap encoder channels check box and retest.

3. Test the second encoder channel.

Let me know the results of the above tests.