Nah PWM fans can be 3 or 4 pin. The 2 Pin fans are the DC ones that are controlled by the Case controllers usually after market ones.
The mobo headers are usually 3 Pin and one or 2 4 Pins , the 4 pin ones are usually for the CPU and the 3 pin ones are usually for the case fans.
Personally, I don't like the Speed Fan utility at all and have advised a lot of people not to use it. The BIOS is capable of handling whatever you throw at it and controlling it optimally without a extra software headache in the rig.
Speed Fan requires the identification of the chipset to be proper, and these identification profiles aren't released by the manufacturer, it's based on the users, sometimes others really make a mess of their rigs by using the closest power profile since their chipset isn't there in the identification box. So I really can't tell you if it's the chipset not correctly identified or the fans not proper.
But, my suggestion is , get rid of that SF utility, it never helped anyone.