Okay, so I have NO idea what just happened, but ...
I plugged the stock cooler into the cpu fan header, and installed easytune again to enable me to easily mess with the fan speed while in windows. I found that it worked - I could speed it up and slow it down as I pleased.
I then proceeded to plug the corsair cooler back in and ... It worked. It is now running silently, and like the stock cooler, I am able to control it freely using easy tune.
Problem solved ... magically.