Perhaps I'm not being clear.
I already CAN run my motor both forward and reverse using a simple VI. The issue is, I'm having to physically switch the pins to switch the rotation direction. I'm at the point now where I'm trying to tackle this using an internal logic (Thus the compare function with case structures). You're suggesting this may be a bad idea, which I accept given you know better. However, you haven't given me an alternative, so I'm stuck.
