Loosing position and need help...

I have a Taig CNC mill powered by G320's, Electrocraft E543 servos
with renco encoders setup in a 2:1 reduction. Running off a P133 in
dos with TurboCNC V3 (not sure exactly what version but its the
latest release of V3)

I'm picking up a few thousandths on long machining files. If I run
an hour long program i could be off by a few thousanths on X or Y,
seems to vary depending on what file i'm running. I've written all
sorts of test files and can never seem to duplicate the problem.

I have no idea whats causing it, tried almost everything to fix it
with no luck and its really starting to turn me off from CNC
machining. I thought I knew enough about this to solve it but no
luck. Have to turn to the experts on here for help.

The fault lights are not comming on, I've tried a different
computer, and shielded cables are used everywhere so picking up
steps is unlikely. Anybody have any suggestions on something else to
try? When I did switch computers, i did keep the same hard drive,
should i format it and start fresh? Anything else?