ideas:
Switch it to metric and see if it moves .010. Write a simple program that goes back and forth, on the guilty axis, with a pause inbetween, so you can watch the display.
Is the .0004 always the same direction? If yes, then it is mechanical? loose encoder coupling, bearing clamp etc.. If it happens both directions then maybe temp parameter, or something else, (Does the minimill do temp comp?)
Encoder counts are usually 10x the minimum resolution or more.
ca