It's probably not the fan controller that's causing your fan issues. It sounds like you have a PWM fan and are trying to control it with a linear fan controller, which you can't do. (Well, technically the controller uses PWM circuitry to control fans in a linear fashion.) PWM fans are controlled by a pulse signal to the fourth wire. From this site:
In addition to the power, ground, and tach signal, 4-wire fans have a PWM input, which is used to control the speed of the fan. Instead of switching the power to the entire fan on and off, only the power to the drive coils is switched, making the tach information available continuously. Switching the coils on and off generates some commutation noise. Driving the coils at rates greater than 20 kHz moves the noise outside of the audible range, so typical PWM fan-drive signals use a rather high frequency (>20 kHz). Another advantage of 4-wire fans is that the fan speed can be controlled at speeds as low as 10% of the fan’s full speed.
You won't be able to accurately control 4-wire PWM fans with a 3-pin controller.

Now, I've never tried this myself (always had 3-pin fans), but in theory that's the gist of it. I'll happily be corrected if someone knows how to get it to work though.