I am not sure that Moonstick2 is correct.
First of all, please check this: I am assuming that your case ventilation fan is a common "3-pin fan" design. That is, there are 3 wires (Black, Red, Yellow) that end in a 3-hole connector that fits onto your mobo's CHA_FAN header. Even if your fan actually has 4 wires coming out to a 4-hole connector, this can work. What you can NOT control by the mobo ports is a fan with only 2 wires that is plugged into a power output connector coming straight from your PSU.
There is one common situation in which a fan runs full speed all the time - that is when you plug a 3-pin fan into a 4-pin port. You are not doing that for your case fan.
The other common cause of this is that there is no attempt to control the voltage going to the fan. This happens when your fan is connected directly to a fixed 12 VDC supply from the PSU's output connectors, OR if the mobo's 3-pin fan port exercises NO control at all.
Now, your mobo's manual says that only the 4-pin CPU_FAN port uses its Q Fan control system, and not the 3-pin mobo CHA_FAN port. That appears to say that the 3-pin port cannot even try to control its fan speed, as Moonstick2 says. That is unusual, but possible. Go into BIOS Setup (see manual p 2-4) by holding down the "Del" key while it is booting until the opening screen of Setup appears. Choose the Power menu and go to the HW Monitor Configuration (manual p 2-18, Section 2.5.5). The manual says there are three items related to CPU temperature and fan speed control, but only one item for MB temperature. Look to see whether there also is a place to configure the MB fan cooling system. If there is, set it to "Standard" or "Automatic" or whatever looks like it does its own control. If there are other options, typically they will be for manually-set fixed speeds. If you can do this, the mobo can control that case ventilation fan's speed (IF it is plugged into the mobo CHA_FAN port) according to a temperature sensor built into the mobo itself. If you can do this, remember to SAVE and EXIT from BIOS Setup. Then disable the Speedfan software so the mobo can have control of that fan, and maybe reboot to get this all working.
If you find no way in BIOS Setup to change the mobo's CHA_FAN action, try another approach. Check the CD of utilities that came with your mobo. There may be an app that runs under Windows that allows you to view, and maybe to control, the fan action. If there is, see if it will allow you to set the CHA_FAN to an automatic control mode.
If neither of these features is available in your system, them Moonstick2 is correct: your mobo simply lacks those features. Your next choice will be a third-party fan controller module that mounts in a front slot. The simpler types of these give you a knob for each fan output connector that you use to manually set a fan speed. There is no automatic control, but you can slow the fans. However, then you must check the mobo temperatures from time to time, decide on what is the "right" temperature", and adjust your fan speed. More complicated units (and more expensive) come with small temperature sensors you can stick to places or components on the mobo so the unit can display those temps. The most complicated ones actually can use those measured temperatures for automatic control. However, before you decide, read user reviews of these systems. Some I have seen say they fail easily.
There is another possibility, but for this you need a 4-pin case ventilation fan (also called PWM fan), and NOT a 3-pin fan. Plus you need an adapter. The adapter allows you to connect both your CPU cooling fan and your case ventilation fan to the CPU_FAN port of your mobo. This puts BOTH fans under the automatic control of your mobo. There is one aspect of this that is not quite "right", but it is OK. The mobo's CPU_FAN port is controlled by the temperature measured inside the CPU chip itself, so it is ideal for controlling cooling of that chip. It is not quite so "right" to use this temperature to control cooling of the case and mobo; however, there is a reasonable correlation between heat generated in the CPU according to workload, and heat generated in mobo components driven by the same workload.
For this purpose there are two options for the adapter. If you have ONLY 2 fans to connect - in your case, one CPU fan and one case fan - then you can use a simple 1-to-2 splitter like this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423160&cm_re=4-pin_fan_splitter-_-12-423-160-_-Product
This is OK because most mobo fan ports can supply power for up to 2 fans, but not more. On the other hand, if you have (or may later add) more than one case fan, use a different type like this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423164&cm_re=4-pin_fan_splitter-_-12-423-164-_-Product
This unit draws fan power direct from a 4-pin Molex power output connector from the PSU so it does not load up the mobo port. However, it works by sharing the PWM signal on Pin #4 of the mobo's CPU_FAN port to all its fans, thus controlling their speed. This is why ALL of the fans attached to it MUST be of the 4-pin type, and it can only work if the mobo port used is a 4-pin type, also. By the way, there is another version of this with one more output connector, which could be used for one CPU fan and up to 3 case fans.
With this last concept of using splitters to control all fans from the CPU port, there is one important point to remember. The mobo REALLY needs to know the speed of the fan that cools the CPU to be sure it is working. So the speed signal from the CPU fan MUST be the one that is fed back to the mobo through the adapter. Now, all fans generate their own speed signal to send back, but a mobo port cannot handle multiple speed signals from several fans - it must get only one fan's speed signal. The adapters I linked to above take care of this because, of the 3 or 4 output connectors for 4-pin fans they provide, only ONE of them has 4 pins; the others have Pin #3 missing. What is important is that YOU arrange that the one output connector with 4 pins is the one you plug the CPU fan into, so that fan's speed signal is the one the mobo receives.
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