Hi Zaccom
Are you sure it was the blue and green wire you changed? What is the wire order now? Because you should NOT swap the blue and green wire! Stepper motors have two coils (effectively two motors in one), and with our wiring they are fed by the green/black (or yellow) wires, and the blue/red wires. You should not mix these up; I'm not sure if it damages the stepper driver, but it won't be good. You can reverse a motor's direction by swapping one pair, or just by reversing the whole plug. Or, more elegantly, by changing your config.g file, as dc42 pointed out.
Ian
RepRapPro tech support