At first sight this looks like a discrepancy on the filter settings for the encoder. Could you please provide more details on which encoder you have and the frequency of the pulses coming into the MID? Do you have any other encoder? Have you tried other axes? If you already received a replacement board from NI, I would suggest you call back on the same service request so we can keep working directly on this issue with you.
When the reading fails you might want to check the encoder with an oscilloscope to see if its outputting clean 90 degrees out of phase TTL signals. Also, you might want to create a LabVIEW program (if you are programming in LV) that will check for the Encoder Position, not the "Read Position" VI, use the "Read Encoder Position" instead. Or in MAX whe
n this happens change to the Advanced tab page in the same 1D interactive and check the 'encoder' reading.
Good luck!
Nestor S.
Nestor