Please use units, I can only assume you are speaking in inches since you said in a post near the top that you haven’t tried mm yet…
I think you are losing 0.006" due to an imperfect conversion factor for the number of steps the stepper rotates and a desire to use/display nice round numbers, a rounding error in the app code, or possibly the problem being visible due to a mismatch/misalignment in the operation of the two stepper motors, not a physical mis-alignment.
I almost exclusively operate in mm and when I step the machine in any direction on the highest resolution (0.01mm on ver3 of carbide motion) it goes like this:
1st press: nothing, reads 0.00
2nd press: moved, reads 0.02
3rd press: nothing, reads 0.02
4th press: nothing, reads 0.02
5th press: moved, reads 0.05
6th press: nothing, reads 0.05
etc.
The end result being four total movements for every 10 button presses, 8 movements for every 20 presses…
So I can infer that the stepper steps every 0.025mm of input value desired, meaning I have a max resolution of 0.03mm in the most ideal case (not accounting for backlash, deflection, mis-alignment, etc). Now 0.006" is 0.1524mm which is well within the resolution I have in mm, maybe there is a rounding error in the calculation/conversion from inches to metric in the app code (or maybe in the firmware though I don’t know if that is even possible).
Maybe try switching over to mm and see what type of movement you observe, see if it gives you greater accuracy in addition to the expected precision, or at least a contrasting case providing better than 0.006" accuracy (that resolves every other step).
Let us know what happens!