I just spent a couple hours "dorking" with it.
Chip, I first changed the Gecko before I decided that I had mechanical problems.
I don't think The gain is too high because I've tried it at zero gain and very low settings. At some settings it goes smoothly in one direction and rattles in the other until it faults.
Brian, I did notice that I did not re-connect the shield to ground, maybe that's it.
Pin 5 is not connected to power, permanently.
After working with it for a while and trying to "turn" with it the problem has gotten much worse and is in one direction.
I started with a .625" rod, using wizard, tried to take it to .575 in .01 cuts. Ended at a measured .545!!!
Adjusted axis tried to go to .525, ended at .480, adjusted again, etc
Final try was when the diameter was down to .380 and this time it wiped out the stock in two cuts!
Between successive tries I made changes in the Gecko gain but other than getting a fault when too high, I didn't see much difference.
So, either I'm gaining steps going in, or losing them coming out.
As I sit here writing this and thinking about what you have written, I'm thinking it is noise.
The signal and motor power are both shielded but the shields are not grounded, and they are bundled.
Tomorrow I'll fix that and if it doesn't help I'll change the encoder. (Grrrrrr)
Thanks so much for all the pointers,
Jerry