I would guess the problem may well be the Breakout board. I suspect you're seeing the upper limit of the step pulse frequency it will pass through, and beyond that point the step pulses are "aliasing", so the frequency coming out of the BOB is lower than the frequency going in. CNC4PC uses some strange pulse-shaping circuitry on their boards that I could see causing that kind of problem if you've got a defective chip or component on the board. It would be instructive to try temporarily wiring up a different breakout board, or even a completely passive one, just on a single drive, and see what happens.
Regards,
Ray L.