Take at look at some of Hoss' videos on backlash compensation.
hossmachine - YouTube
Check to make sure you have no slack on the thrust bearings. Move each axis several times back and forth a set distance and make sure it always returns to the same pos to make sure you are not loosing steps.
If I'm not mistaken, stock screws have linearity errors so different sections may have slightly different backlash amount as the threads may not be evenly spaced along its length.
I'm also looking to make PCBs on my mill as soon as I solve a few tech issues of my own. What software are you using to generate the gcode from the gerber files?