Multiple case fans on one motherboard header

Two PWM fans on a spliter is completley fine, even if different sizes.

No because in the splitter it should be missing pin 3 for the tach signal on the second fan.

If you zoom in on the second picture you can see that the top right one only has 3 wires going to it.
Trust me, one of the 2 only has wires to pins 1,2, and 4.

I can understand how you got confused. There is a lot of misunderstanding contained in some posts about fan systems, so let me help clear things up.

Almost all fan headers on mobos can supply up to 1.0 amps current in total to all the fans connected to that one header. On some newer mobos now I am seeing special headers labelled H_AMP_FAN that can supply up to 3.0 amps, but they are not the "common" ones. Your mobo says its CPU_FAN header can supply up to 2.0 amps, but that does NOT apply to the CHA_FAN header.

Your mobo has three fan headers, and each does a different job, so don't confuse them. The CPU_FAN header normally is used only for power and control of the cooler for your CPU chip. It is based on a temperature sensor inside the CPU chip itself that feeds a signal to the mobo on one pin of the chip. The PWR_FAN header very likely is of no use to you. It is intended solely for use when your PSU has a special set of three wires coming out that end in a female 3-pin fan connector that can plug into the PWR_FAN header. Is only function is supposed to be to allow your PSU to send its fan's speed signal to your mobo so it can be displayed. The intent is that, if your PSU does not have this set of signal leads, you connect NOTHING to the PWR_FAN header. Now, it happens that the mobo actually does have Ground and a fixed +12 VDC on its first two pins, so it CAN be used to provide power to a fan, BUT there will be no control available - it will always run the fan at full speed. The header of interest for this thread is the CHA_FAN header. Its fan control is tied to a different temperature sensor built into the mobo, so it is the place to connect case ventilation fans.

There are two basic types of fan designs used widely in computers now. 3-pin fans are older. The signals on the mobo header being fed to the fan are Ground (Black wire) on Pin #1, +DCV (red wire) on Pin #2, and Speed Pulses (Yellow wire) on Pin #3. The voltage on Pin #2 is varied by the mobo, from 12 VDC max down to about 5 VDC min usually, to control the fan's speed. The fan motor itself generates a speed signal of two pulses per revolution and sends that back to the mobo on Pin #3. The mobo can display that for you and will monitor it for failure detection. But it does not actually USE that signal to control the fan speed.

The newer system is 4-pin fans. Mechanically and electrically the signals and pins are very similar, so you CAN connect any 3-pin fan to any 4-pin header, and the other way around. The fan will work, but with some limitations when you mis-match them. The header for a 4-pin fan IF it actually uses the true 4-pin PWM method of control, has these signals (not mentioning colours here because they are different from 3-pin system): Pin #1 is Ground again, Pin #2 is a fixed +12 VDC, Pin#3 is for the Speed Pulse signal again, and the added Pin #4 is the PWM signal going to the fan motor. Inside fans of this type there is a small chip that uses the PWM signal to modify the flow of current from Pin #2 to the motor windings, turning it on and off very quickly (at about 20 kHz) to reduce the average current through the motor and thus changing its speed.

Now, what happens if you mis-match fan type to header type? Plug a 3-pin fan into a 4-pin header and the fan receives a fixed 12 VDC on Pin #2 at all times, but it does not receive (nor could it use) the PWM signal, so the fan always runs full speed. It cools, but there's no control. The other way: plug a 4-pin fan into a 3-pin header. That fan does not receive any PWM signal so its internal chip cannot modify the power supplied on Pin #2. BUT that pin is supplying a VARYING voltage, so the fan's speed DOES change, and the mobo can control it. This form of control of a 4-pin fan is not ideal, but it works.

Here's where a lot of confusion can start. First, any 3-pin fan header can ONLY operate in the older Voltage Control Mode. On MANY mobos now the fan headers all have 4 pins, but they do not always work as 4-pin headers! Some actually use only the 3-pin method called Voltage Control Mode or DC Mode for control, and never send out a PWM signal on Pin #4. As you can see from above, this WILL accomplish speed control of either design of fan, so it's kind of "universal" even though it fails to use the advantages of the new PWM fan design. This type of header does cause a problem, though, if you are trying to use a 4-pin Hub to connect several fans to one header, because such devices MUST have a PWM signal on Pin #4.

On better mobos today you often will find that in BIOS Setup you are given a choice of how a mobo fan header controls its fans. You can set whether it uses the older Voltage Control Mode (aka DC Mode) or the newer PWM Mode. A few even claim that they are self-configuring and can automatically detect which type of fan is connected and set themselves.

One more background point which actually IS pertinent to your case. A mobo header can accept and handle the speed pulse signal from only ONE fan on Pin #3. So, any proper Splitter or Hub will only send back to the header ONE fan's speed signal, and not connect the other one. Some earlier Splitters were made wrong and connected both fan's signals back to the mobo, causing them to get very confused with double the pulses coming in and at wildly changing timings. The Splitter you gave a link to is done this wrong way (as you say, it has all pins on both outputs) and that is why your mobo is showing you wildly swinging speed readings when you use it with two fans. I'll outline a fix later.

Your mobo has only one CHA_FAN header to use. In the manual on p. 1-27 the label on Pin #4 is not at all clear, and there is no other clear statement about the control method this header uses. However, both of those Coolermaster fans are true 4-pin units, so they CAN be powered and controlled by either type of mobo header. Moreover, they each are spec'd at 0.26 amps, so the total load is 0.52 amps, and there is no problem connecting both of them to a single header using a Splitter.

The last problem is the construction of your Splitter and the way it is causing fluctuating fan speed readings. You can fix this by cutting one of the wires to Pin #3 of one of the output arms. You'll have to slit back the outer covering a little to get to it. When you're done, ensure the end connected back to the female connector (the one that plugs into the mobo) is not able to short out some place. To identify which wire, look at the output connectors. There is a plastic "tongue" on one side aligned with the first three pins, and a gap over the 4th pin. So you can identify Pin #3 and snip the wire doing to that pin on ONE of the two male output connectors. You will never "see" the speed of the fan plugged into that one, but that's OK.

The mobo does NOT try to control the speeds of all the fans on a header to be the same. In fact, as I said, it does not even worry what the speed is (except for failure detection, which is not part of speed control). The header simply sends a power supply on Pin #2 and a PWM signal on Pin #4 and whatever speed that delivers in any fan is OK as far as the mobo is concerned. If they don't match because the two fans are of different designs, it does not care. In fact, the truth is that the automatic fan control systems are NOT paying attention to fan speed. The are trying to ensure that the TEMPERATURES at the relevant sensors are correct, and they merely change the power going out to their fans to alter the cooling they give, thus keeping the temperatures under control.

Second query first. If you snip of the lead to Pin #3 of ONE output arm of the splitter, that won't change the way the fan is controlled. All that will do is prevent the confusion the mobo is experiencing now because of two fan speed signals overlapping.

You speak of a "spare 3-pin fan" and of an 80 mm fan mounted as front intake. Are those two different fans, or just the same one?

You linked to a mobo web page but then commented that your actual mobo is a slightly different model with "two headers". The manual in the link has three headers in total, one each of three types as I outlined above. Does yours actually have a FOURTH header? Or THREE? what are their labels?

Then you say you plugged that "into a 4-pin header". What header? As I said, the manual says your mobo has only one CHA_FAN header and it has 4 pins and appears to be using true 4-pin PWM Mode. So, are both the 92 mm 4-pin PWM unit and the 3-pin 80 mm fan connected to that one CHA_FAN header by using the Splitter?

If a 3-pin fan is plugged into a 4-pin header that actually is using PWM Mode for control, then it will only run at full speed. However, you say when plugged into "a 4-pin header" it appears to run at only half speed, and when plugged into a PSU output it runs noticeably faster. Again, I wonder what 4-pin header? And, how is that header configured in BIOS Setup? There could be a setting that limits its speed, or it could be using the wrong temperature sensor.

If you connect both of your 4-pin Coolermaster fans (80 and 92 mm) to the Splitter and thereby to the CHA_FAN header, they both should change their speeds together. Doing that with that Coolermaster 80 mm unit at the front would then improve things.

Now another idea to consider. Do you have room in the case front to mount both of your 80mm fans? Since you seem to have somewhat inadequate cooling now, this could improve that. You mount both in the front as intakes. Connect the 3-pin spare one to that "PWR_FAN" header I told you not to use. Then it will run at full speed all the time because that header does no control. Connect the two Coolermaster PWM fans (80 mm front intake, 92 mm rear exhaust) via the modified splitter to the CHA_FAN header and their speeds will be automatically controlled by the mobo. You'll get a sort of "base level" ventilation with the full-speed 3-pin fan plus controlled additional ventilation from the other two.