Its hard to see how well you are doing on that scale by trying to see the small difference between the red and blue plots.
Zooming in or plotting position error would show much more.
Better yet if you include the data so we can zoom in and re-plot it however we wish.
Instead of taking a photograph - take a screen capture with Alt-Print Screen, then paste into something like Paint, and save as a *.png file.
The output (green plot) needs to go to ~900 for your test motion. Your limit on the Integrator of 500 means that the Integrator will likely saturate and stop helping at some speed. Probably a Max Limit I of 2000 would be better.
You didn't show us your Filter Settings. Usually a 2nd Order Low Pass filter Freq=1000 Q=1.4 in the 3rd filter is helpful.
Your Velocity of 4 million counts/sec is way too high. Max encoder count rate of KFLOP is 1 million counts/sec. The motion you are testing is only reaching 300,000 counts/sec because of the relatively short move distance and limited Acceleration and Jerk. You might read this article:
Instead of taking pho