Normally the BIOS allows you to set the target temp, i.e. 40C. This means the fan should run at the percentage set until your CPU gets to 40C. Once it goes beyond 40C, the fan will spool up above the percentage speed you set. Thispercentage fan speed setting will only becomes visible when you set a target temp i.e. you go to manually setting the fan behaviour.
As for Speedfan, it can only control fans that are controlled by Fintek chips that have been programmed into the Speedfan code. Speedfan is developed by an individual and he can't keep up programming all possible chips in the market. He usually tests the most popular boards and expects feedback from users like you. You will see in Speedfan how to compile a dump file and then send it to the developer. If he gets the time, he may analyse it and try to help you.
There is that remote possibility that your board has a faulty PWM control circuit/chip or even the PWM control circuit of your cooling fan itself. You would need to test the fan on another board to see if it works or not. If it does, then you know where to start investigating next.