Certainly sounds like lost steps.
You should review the wiki (http://wiki.linuxcnc.org/cgi-bin/emc...StepGeneration) for setting up steppers and make sure you did not skip any of the steps.
Take the time to carefully verify your computer's latency and remove any binding issues in your machine.
I as of late have had difficulty with my X axis (48" long) developing a tight spot aroun X=0-4". I lose steps in the area very easily. I still have not completely figured out the problem, but its probably a combination of leadscrew whipping and binding on my pipe side rails.