Your swap test indicates that whatever's going on, it isn't the fault of the software, controller or breakout board. That leaves the motor, plus its wiring and cable. Double-check to make sure the wiring is correct and well-attached. Assuming a 4-wire motor, there should be two phases with continuity between them. (a six-wire motor works basically the same way, but there's a center tap which can be connected so as to give you the choice of parallel or series operation). A stepper motor works by energizing one phase at a time, pushing the armature from one position or "step" to the next one, that's typically 1.8 degrees apart. When the motor changes direction, the phases change their pattern of energizing the internal electromagnets and push the other way. It sounds like one of those phases isn't operating correctly, so you're only getting half the control you need. A faulty cable can cause that, as can mis-wiring, a bad motor, bad grounding or electrical interference.

Andrew Werby
www.computersculpture.com