Mesa 7i77 output scale

Actually it looks a bit like bad stiction when you start (since its much worse when starting from a static position)
can you plot the initial velocity ramp with a faster sweep time (maybe 20 ms/division) and add the pid output to the traces?

EDIT:
Also since these are linear scales (I just noticed), any backlash (ballscrew, gear,coupling etc) may show up as this kind of an error
At the relatively low acceleration of 60 mm/S^2 you will have moved only 3 microns in 10 ms. If your backlash is in this region (~3 microns)
your plots are as expected.

Note that if you had just used the rotary encoders or emulated encoders from the drives, the plots would probably look much better
its just that with linear encoders, all the mechanical flaws are visible.