[Jared Russell]

My suspects would be, in order:

1. Mechanical slippage between the encoder and the shaft whose rotation it is measuring (you seem fairly sure that this isn't the issue, and I believe you, but in general it is the first/easiest thing to check)

2. Improper spacing between the optical disc and the encoder circuitry. Use a spacer tool when installing the disc.

3. A "smudge" (fingerprint or scratch) on the disc that causes one of the photoreflectors to miss a count or two per revolution. Easiest solution: try another encoder disc.

4. EMI/wiring problem.

5. Code issue. Your code doesn't ever reset the encoder, does it?

6. An absurd pulse frequency (too high of a CPR on the encoder given the speed of the shaft it is measuring). However, in the cRIO era, you need to be well into the tens-of-thousands of pulses per second before this would be an issue, so it is unlikely.