Assuming you're talking about your Gigabyte board, you don't need pwm fans since the casefanheaders only support voltage control. Not sure why they use 4-pin headers since the 4th pin isn't connected at all.
Thanks for the info. I found out that the motherboard automatically does fan control, but you have to set the mode to voltage. SYS fans 1/3 are voltage control, sys fan 2 is not. I So when I tested it before I had a fan on 2, and I also never set the fans to voltage control.
I checked an old version of the manual but in the new revision it's indeed indicated that sysfan 2 has pwm control but no voltage control.
Are you sure about the motherboard actually changing fanspeeds? The Gigabyte boards I used ran the fans at a constant 50% no matter the thermals.