Check the current going to the extruder stepper. Mine did this when it was under-powered.
Not sure what controller or stepper drivers you are using, but here's the documentation on adjusting stepper current for a Melzi w/integrated stepper drivers.
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reprap.org]
I ended up manually adjusting the potentiometer for the current to the extruder stepper while the printer was printing and skipping. I turned it down ever so slightly, skipping/stuttering got worse, then adjusted it up in small increments until the skipping stopped. I adjusted it downward again until the skipping started, then up just a hair. Extruder stepper runs slightly warm now instead of room temperature. Haven't had any more issues with the extruder stepper since, it does what it is told to now. :-)
Ground yourself and use insulated tools.
-speedeep