At the moment, encoder values are only read from PoKeys. Although the values of the encoders (except the Ultra Fast one) can be set to any value, we tried to minimize the number of commands sent to PoKeys device to improve the response times of the device. We can add a predefined fixed DRO value offset to each encoder.
I don't really understand your last question - you mean that although the index input is high, the encoder is not counting?
The 0-1-0-1 sequence also indicates that only one of the encoder inputs receives pulses - please check your connections and pins (Ultra fast encoder connects to pins 8 and 12, 13 is the index input).