So not knowing how the loop actualy works ,then the only thing one can do is adjust the machine to get it as good as possible, and then find the appropriate velocity and acceleration settings that
provide for reliability.
It's tough to adjust to get "good as possible" unless you measure. If you have a torque indicator you can adjust the gibs, bearing preload, etc. and see the affect of the adjustments.
ie; tight may mean it takes say 60 in oz to rotate the screw as compared to loose which may mean 20 in oz required. Now when running fast and your at the upper end of the stepper speed
there is not much torque left , so say you only have 60 available and if tight, you have nothing left for machining, and the stepper is likely to skip no matter what control is used.
Just making the point that, without an adjusted machine , software settings or controls are not true to their intended use.
RICH