Arturo,
Could be, but i would bypass the BOB if the drives are optoisolated and see if there is a different axis behavior.
nucular,
Do you get the same affect when using the X & Y axis?
Acceleration setting is different than velocity. First you find the max velocity at a low acceleration and then increase the acceleration to find the max acceleration relative to the max velocity and you don't use either at the max. You reduce them. You want reliable motion over a variety of conditions.
Actualy what you want is power, so the velocity setting may be much lower as that puts the max velocity / speed setting at the highest torgue relative to motor speed / rpm. All somewhat of a trade off i may add.
RICH