Hi Scott,
I would check the voltage applied to the direction output for the individual axis on the breakout board.
ie if you have to change the direction on an axis measure what the direction pin has changed to, note the reading ,high or low, power off then on again and see what the reading is now. I am not sure how mach3 works at power up will it put a pin high.

I thought the normal thing if the stepper was going in the wrong direction was to swap one of the pairs of wires over, I am not sure in what state the pins would be when you power up in my view they would normally all be low.
POINT to remember if you change the wires to the steppers TURN the power off first as you could blow the drivers.
If in doubt you ask a question on the mach3 forum.

Peter