The manual would indicate that your board does not control the speed of 3 pin fans. This is why it is always loud.
Your options are to.
A. get a fan controller(would allow you to adjust the speed to whatever you want) or fan speed adjustment cable(most give you at least an option to run the fan at 5 volts[much slower and some fans do not start on 5 volts, but will always ruin that speed]) Some even give you 7 volts as an option. Placing a 50 ohm resistor in line with the fans power would also slow it down to about 1200-1400 for most fans of that speed.
B. Get a PWM fan(like the NF F12, SP120 or even CoolerMaster Blade Master 120) OR get a quieter fan that you can stand to hear at full speed.
C. Build a PWM to Voltage converter. This is a DIY Project and only recommended if you like DIY stuff.
Link1 A high gain transistor or 2 in a Darlington configuration is required (the plans withe Zener Diode on page 2 do not need high gain transistors)
Link2 This guy makes and sells adapters, no clue what the shipping would cost. He also has the plans showing. A higher gain transistor never hurts with this plan as well