I vote with Hood. I've personally experienced the same problem, even with new anti-backlash nuts. Tracked it down to a combination of machine flex and sticky axis bushings on my machine, but it can be any of several mechanical problems. It is not a Mach3 problem. Disconnect the axis drive and see if it moves smoothly end to end by hand.
Please let us know what you find.
Regards,
John Champlain
www.picengrave.com