The motherboard (Gigabyte Z77-D3H) controls my 3-pin CPU fan just fine. My system fans are a 3-pin fan (plugged into SYS_FAN1), and a 4-pin fan plugged into SYS_FAN3. All 3 of the system fan headers are 4-pin, but the user manual states that SYS_FAN1 is really a 3-pin header (that it can control the speed of a 3-pin fan) and the 4th pin is just a reserve. All my fans have a max RPM of 2000.
Normally, all the fans run around 1000 RPMs when I'm not doing anything intensive. This proves that the motherboard can set the speed. However,when I run Folding@Home and my temperatures increase (around 70C) only the CPU fan increases to around 2000 RPMs. The system fans stay around 1000 RPMs. Through the BIOS I am able to disable the system fan control and the system fans then run at max RPMs (meaning the motherboard was doing something).
I've updated the BIOS to the latest version and tried out Speedfan, but neither helped my situation. What I'd like is for the system fans to ramp up their RPMs as needed. Any thoughts?
Tl;dr: My system (case) fans, but not my CPU fan, are always stuck around 1000 RPMs out of 2000 no matter the temperature. I have both voltage (3-pin) controlled and PWM controlled (4-pin) fans plugged into my motherboard as system fans.
Best Answer
The case fans have nothing to do with cooling the CPU. That's a job for the CPU fan. The case fans merely circulate air by introducing fresh outside air, and exhausting stale, hot air. Thus, what you're experiencing seems right. The CPU fan increases speed to keep CPU cool, but the system temperature (not CPU temperature) is not high enough to trigger increase in case fan speed. If you operated your PC in a hot environment, the case fan speed should (assuming your motherboard has a "system" thermal sensor) increase.
This is the general rule of thumb. Of course, different manufacturers may have different cooling control systems implemented into their BIOS. Harrymc's answer is valid too