When swapping the Y and Z axis, are you swapping the driver and the motor (i.e. just swapping the driver inputs) or one component at a time? There could be a mis-wired connection between the driver and the motor itself. If you haven't already done so, swap the actual drivers between the Y and the Z both at the input from the breakout board (you are using one and not trying to run the drivers directly from the 25-pin connector, right?) AND the output to the motor. If the symptom switches from one axis to the other, then it's the driver. If not, check the motor wiring.
However, as was stated by TOTALLYRC, it's probably the driver as a mis-wired motor would usually have bad steps which you'd notice (usually by sound) or it could be a faulty breakout board. Just something else to check before spending money on a driver if that's not the issue.
Stephen "Highspeed" Kruse