I have been working on the homing problems with the PPMC driver, and may have finally solved the problem. I had the sensing of the index pulse level-sensitive, but the zeroing of the encoder count when index-enable is set true was edge-triggered. I didn't see a way the software could get in fast enough to see one without the other, but apparently that was happening. I have put a digitally noise-filtered edge-triggered index pulse to both the index sensing and the zero on index logic, and it seems to be working better. It all is working with the current development head version of the driver.
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