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We are having a similar problem with position control with the same encoder on our gatherer. Sometimes it works fine, and goes to the setpoint perfectly both physically and digitally. But seemingly randomly, the setpoint is correct digitally, but the gatherer is in the completely wrong position physically, making it seem like the arm is moving without updating encoder values. The encoders are plugged directly into the DIO ports on the roborio. We have also tried swapping cables, encoders, and motors. It seems to make no difference.
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