It doesn't matter - does it
Backlash is that number of pulses the computer puts out, where the axis does not move. As long as the computer calculates the number of pulses correctly, including that required by backlash, then it will arrive at the right point. If you are saying that the computer moves your axis back by 1 mm before adding the backlash - how can it
The computer puts out the pulses, and the axis does not move until the basklash is taken up, the gears are bedded in and got their shoulders to the table ready to shove the other way.
Mach 3 deals with backlash in a funny way, and it is a little bit disconcerting. The axis appears to move, the backlash then is applied (usually at a different frequency so you hear it) then the movement continues - three distinct sounds. You can adjust the speed of your backlash if you wish (on the backlash page).
Are you saying by this that your backlash is incorrect becaue in my experience, although the way backlash is applied is a bit odd, it is still accurate.