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In the manual the chassis fan header diagram shows +5V on the 4th pin. 5V on the PWM pin means 100% duty cycle, so it then would use voltage control like a 3-pin fan to control the speed.


What has happened several times now is Asus reps will claim it's an error in the manual and they'll correct it later. They said that about the Maximus VII Impact but it turned out that the chassis headers are DC control only. The manual has been updated since it's release but it still shows DC only on the chassis headers.


I specifically asked about the X99-A when it was announced and got the same story. I ended up using that board for a customer's build at work a month or two ago and tested it briefly. I didn't have my multimeter on me though and was in a hurry to finish the build but I tried my Noctua 120mm Industrial fan and the controllable RPM range on the chassis header was good, but not quite as wide as the CPU header so there's something going on there.


It's not just Asus though, Gigabyte is just as bad. If I can gather enough motherboards to test I'd like to get an oscilloscope and test them all and record the results to find out just how many boards, if any, truly have PWM chassis headers.