Fan headers not working properly ?

If they are controlled by PWM only(4 pin)than it cannot control voltage controlled fans(3 pin). Some boards do voltage control and PWM. Read your manual. there is no "sensor" for three pin connectors, that is nonsense. They are either PWM fans or they are not

The CPU fan header is PWM. The SYS_fan headers are not PWM; they have the fourth pin but it doesn't do anything. They use voltage to control the fan speed. It is possible, if you have really really bad fans, that there isn't much gradience in their voltage to speed. But, much more likely is the software. My experience, the bios software asus uses for controlling the sys_fan headers is garbage. The flip side though is that the Windows software they use (fan_expert) is great; easily the best I have ever used. I suggest you install the software they have as it really is great for fan speed control.

Well you have to calibrate the software for it to work. When you install it you go to the fan expert tab or whatever it is called and do the fan tuning. It is going to run and turn on and off all your fans. Then when it is finished, you can either let it control the fan, or click on each fan, change it from smart to manual, and you can set the exact RPM you want.

The other option is to get a fan controller.

Hmm....do you have the fan type selected as advanced in the bios? for 3 pin fans you have to change it to advanced for it to work properly (some fans work anyway but not all, not sure why some work and not others). If that still doesn't work than I would just pick up a cheap fan controller as a last resort.

Incidentally yes if your PC is nice and cool it will turn the case fans all the way down and in some cases off; you can change the threshholds though.
All in all, not sure why the software isn't working for you.

I, too, am puzzled that you cannot get your mobo to change any fan speed. First, a quick review of what should happen.

If you connect a 3-pin fan to a true 4-pin socket on the mobo, that fan will always run at full speed. There are SOME mobos that allow you to set in BIOS whether the fan port is operated as a 3-pin or a 4-pin port, and even SOME that figure this out automatically. Your mobo's manual makes no such claim, so it is possible that all 3 of these ports are simply 4-pin ports, and they will behave this way.

Now, Deuce65 claims the two SYS_FAN ports are fake 4-pin that really are only 3-pin. I've never heard of that, but it's possible.

OK, in your manual, Section 2.7.4 on p. 2-34, it deals with the CPU Q-Fan setup. First, you have to Enable it. Then you select a Fan Profile, and "Standard"should provide automatic fan speed adjustments based on the internal CPU temperature. In this mode the fan will START up at full speed for only a few seconds, then slow down and change from time to time as CPU workload changes. "Silent" or "Turbo" should give you either very slow or full speed. Oddly, "Manual" does not let you set a fixed speed manually. Instead it allows you to set up your own parameters for automatic speed control. You get to set the maximum fan speed and the CPU temperature that will trigger that high speed, and the minimum fan speed and the CPU low temp that will do that. At intermediate CPU temps the fan speed will be scaled between those two points.

In Section 2.7.5 on p. 2-35 you see the same settings for the two SYS_FAN ports (it appears they both operate from one group of settings). Again, you must Enable the Q-Fan control first, then choose a Fan Profile.

There is no way in any of these for you to set a fixed fan speed of your own choosing. The closest is the choice of fixed low speed ("Silent") or fixed high speed ("Turbo").

If your fans do not perform as I just outlined but keep running at full speed, then you cannot achieve automatic fan speed control using your 3-pin fans on these 4-pin headers. In that case you will have three options:

1. Let all the fans run full speed all the time.
2. But one or more 4-pin fans and replace some of yours so the mobo can control the 4-pin units properly.
3. Buy a fan controller unit that mounts in your case. This will give you very different control options, as follows.

When you use a separate fan controller, your mobo has NO control of the fans, and it knows NOTHING about fan speeds, because the fans are NOT connected to the mobo in any way. A 3- or 4-pin fan generates a pulse train signal that it sends back on one wire to the fan port it is connected to, where it can be counted to display fan speed. If the fan is plugged into the mobo, the BIOS does the speed measurement and display. If the fan is connected to a separate controller, the mobo has NO fan speed signal and it ignores that question. Now, the controller MAY do its own fan speed display if it has that feature, or it may not.

The automatic speed control system on the mobo uses temperature sensors (one built into the CPU, one on the mobo) and alters the respective fan's speed by comparing those measured values to targets. A separate fan controller has NO access to those two temp sensors, so it cannot do that job. In general, separate controllers allow you to manually set a fixed fan speed with a control knob for each fan connected, and it is up to you to determine whether to change that setting. Some controllers actually include their own temperature sensors you can place on your mobo so they can display those results to you. I think there may even be a few that try to use automatic control the way the mobo does. BUT they cannot get the correct temperature readings to use, so they don't do that well. For example, how could you place a temp sensor probe inside the sealed case of the CPU?

So, if you want to keep your 3-pin fans and control their speeds, you can do that by buying a separate fan controller and manually setting speeds.