Thanks. That doesn't actually solve my problem though, however Gigabyte have since given me the answer.
Bascially, there were two problems:
SYS_FAN1 supports 3 pin fans, but SYS_FAN2 and SYS_FAN3 can only control the speed of 4 pin fans, which I find rather odd. If you use a 3 pin fan in these headers it constantly runs at 100%.
Although there are 3 system fan headers, you CANNOT control these independant. If sys_fan1 runs at 50%, then 2 and 3 also run at the same speed.
Which is fine, I've only got 2 case fans anyway - they're both 3 pin so I'm running them (and controlling them, albeit not independantly) both from sys_fan1 with a splitter cable.
Are you running a later rev of the motherboard? Mine only has SYS_FAN1 and SYS_FAN2, and like you said, SYS_FAN1 only supports voltage control, while SYS_FAN2 only supports PWM. I have three 3-pin 120 mm case fans that I hook up to SYS_FAN1 using a 3-way splitter.
My experiences with the PWMs in SpeedFan differs from the reviewer's. I don't have anything hooked up to SYS_FAN2 so I have no idea how the PWMs affect that.
- PWM1 appears to control the CPU fan using voltage control--I can slow down the CPU fan as low as about 200 rpm, and then it suddenly stops spinning and won't start up again unless I "jolt" it by setting PWM1 back up to something quite a bit higher, starting it back up at about 600 rpm.
- PWM2 controls SYS_FAN1, which is only voltage control.
- PWM3 appears to control the CPU fan using PWM control--I can't slow down the CPU fan below about 400 rpm, even if I keep decreasing the PWM value.
If I had to guess, I think PWM1 is controlling the voltage (3rd pin) for both CPU_FAN and SYS_FAN2, while PWM3 would be controlling the PWM (4th pin) for both CPU_FAN and SYS_FAN2. Since I'm not using SYS_FAN2, this doesn't affect me, and I can use PWM2 and PWM3 to do all the fan control I need.
I use advanced controls to set the CPU fan speed according to both the CPU temp and the system temp. As the review mentions, the VRM chips get hot, so the system temp is often higher than I'd like. I run a Big Shuriken 2 as my CPU cooler so there is some spillover hitting the VRM chips. Thus I run the CPU fan faster than necessitated by just the CPU temp when the system temp is high. At under 1400 rpm I can't hear the CPU fan, so no problems there.