I just bought this board this week and installed it with a SilenX low profile 3-wire CPU fan
You cannot control fan speed with 3 wires. A 3-wire fan uses 2 wires for power and the third wire reports rotation speed. You need a 4th wire to control fan speed.
Perhaps this is the case for this board. I have used 3-wire fans on older Gigabyte boards and was able to configure different speeds. If this board can only support PWM for fan speed control then I'll find an alternative cooler.