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I am still looking into this, I did make a small change to the encoder driver to simplify
the index spacing detection. (I added the option to not zero the position on index detection)
This should simplify the distance coded index detection hal component, otherwise I would
have needed to undo the encoder position zeroing in the hal component, and that was pretty ugly. 

I would try setting the following errors wider so you can see the actual behavior without getting an instant following error
(say 25 and 25 mm)

Then first set the PID up with all terms 0 except a small amount of P

Then check if the motors roughly hold position and move when jogged

 

Please read the post fully to understand why this is necessary.

I will get this posted as soon as I can. Thank you.