Did you check to see what you have in the parameters for backlash? If it's too large, i.e. more than you have backlash in the screw to nut, then you would get a jump like you describe.
Mine had none because we replaced the computer and had to input the parameters by hand, so once I got it running I checked for backlash with an indicator and then added the amount in to that parameter, now I can traverse an axis change without any blips in the surface.


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I could use a secound mill running , so , I tought before I scrap this thing I'd give it some more looking into 



