Hi Dave,
I suspect what is happening is that your system (Motors, Amps, or Supply) is just not capable of the feedrate you are commanding. If a trajectory is commanded faster than what the system can move then the motors fall way behind the trajectory while going as fast as they can. Eventually when the trajectory slows down then the motors catch up to where they are supposed to be.
Normally this would cause a following error fault but it looks like you have the Max Following Error set at 1 billion.
You should test high speed moves using the KMotion Step Response Screen. The Plots you posted were of very tiny moves - 4000 counts. Your system has very high resolution - 160,000 counts/inch, so this is only 0.025 inches which is not enough distance to accelerate up to any speed.
Try much larger moves and you should see the problem clearly. You can plot Velocity to easily see what speeds you are getting up to.
Your Max Jerk setting is quite low. The numeric value is almost the same as the Max Acceleration which means it would take almost a full second to apply full acceleration. A more reasonable value might be 50X the acceleration which would apply full force in 1/50th of a second.
You will probably see that for large fast moves that the output (green plot) is saturated at max output of 10V yet the motor continues moving at a slower speed. There may just be a setting in the Amp limiting the speed.
Your Bode plots and small moves look quite good. I wouldn't expect following errors of +/- 1 count. 10 counts with 160,000 counts/inch resolution is only 60 microinches.
HTH