The encoder signals "step" half way through the wave instead of being complete square waves.
Put a termination resistor between the A+ and A- (or B+ and B-)...probably 120 Ohm.
The 6K Hardware Installation shows a 243 Ohm termination resistor. That is incorrect. The Addendum correctly shows this differently as NOT having a termination resistor at all.
Some encoders require a termination resistor. For instance, the Heidenhain encoders prefer about 120 Ohm termination resistors.