Do you really think that it matters? I mean, that is off by 0.0013mm, or 1.3 micrometer. That is very good and extremely difficult to measure accurately.
I suspect that it is caused by your steps per value and that depends on your pitch as well as micro stepping. It may be so that it is not possible to calculate the number of steps more precisely for 100mm so Mach3 calculates the nearest. What are your values for those three?