I have decided to bypass the onboard extruder stepper motor control to use a separate Pololu stepper driver to run the extruder stepper motor. The reason for this stems from the original RepRap which was designed to use a DC motor for the extruder and not a stepper motor, therefore used some electronic trickery to control the speed. Using some clever programming they hacked the driver to control stepper motors.
However this is now what is causing my stepper motor to emit that high pitched noise. It is possible to bypass the information sent from the motherboard to a separate stepper controller, and leave the extruder board to just control the hot end. This method is documented on the RepRap wiki and suggested in a couple of forum posts I have seen.
I have made a carrier for the Pololu board from strip board using Tony Buser’s layout as a guide (http://www.thingiverse.com/thing:3761). I ended up changing it a bit as I wanted screw terminals for the power and motor connection and not headers. As the screw terminal spacings are wider than the header’s I had to use more short jumpers to get everything wired correctly. I have tested it and it seems to work very well. It is now much quieter and the motor seem to run a bit cooler.