Gaining steps somewhere

I just getting this cnc mill together..I note that after a series of 8
rapid go's to 1. and slow downfeeds to -.500 I end up with the endmill
being positive by nearly a 16th inch...This mill is using servo motors
with encoders..Also Mach2 , Rutex drives and Campbell's breakout
board..The encoder on that motor takes 20,000 pulses to move the Z axis
one inch.I should think that was pretty high resolution.
I discovered this circumstance while running a small engraving test
program..I didnt look to see if it calls for absolute or incremental
positioning but I think that hardly matters as this behavior isnt right
irregardless.Anybody have an idea whats happening here?
Steven