First, if your converting an old knee mill you will NOT get 0.0001" accuracy. Even if you add brand new fancy ball screws and such you'll see more error from cutter deflection, cutter wear, material changing size as it heats/cools, etc, etc.
Second, Mach will always send out enough pulses to go where you tell it to within the resolution of your steps/unit. If you only have 2,000 steps/unit then you will see some non-cumulative rounding issues at certain numbers (as everything is broken down into 1/2000" increments). Again, lets stop and consider what that 0.0001 means in the real world...unless you have a very hi precision machine, operating in a temperature controlled environment, that you have done screw mapping on, let warm up to two hours before cutting parts,etc, etc; you just won't see it.