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If you can get LInuxCNC running, I would first verify the home switch operation
with halshow.

 

It looks to me like the FF1 term is different (too low) in the plots where the following
error tracks the velocity (higher velocity plots) Did you change some drive parameter
in these plots?

Also note that the velocity is not higher in the 6000 mm/m plots as it only gets to ~50 mm/s
(3000 mm/m) because of the acceleration bound