I used to have that also.
Two things that casued this was:
Heat. My smoothstepper is connected to a GeckoDrive G450, and that got hot. A fan that pushed air under the geckodrive fixed that.
Changing feed rate above 100% while running. That is a big no-no.
From their FAQ:
With Mach3, NEVER run your Feed Rate Override above 100%, only use it to slow down your feedrate. If you want to go faster, regenerate your G-Code from your CAD/CAM software. Running your FRO above 100% will cause jerkiness and misshaped circles.
Make sure that you run Mach3 version 3.043.062