Jason,
This is normal behavior for this board. There are two ways that the speed of a 2- or 3-wire fan can be controlled. The most common method used today is to vary the voltage provided to the fan (the lower the voltage, the lower the fan speed). The older alternative is to send the power to the fan in pulses (the fewer pulses delivered, the lower the fan speed). This latter solution, which was used on the BX2 board and many of its predecessors, can provide better control of fans at lower speeds, but, depending upon the fan used, can have the side-effect of creating a "ticking" noise that can be irritating -- and it does cause fans with LEDs to flicker as you are seeing. Unless you like the flickering LEDs, the only recommendation I can give is to (a) not use fans with LEDs or (b) remove/disconnect these LEDs.
...Scott