First, there's nothing wrong with the Splitter you describe. Any mobo header can deal with the speed signal sent back to it from only ONE fan. So any Splitter will send back the speed of ONE fan (using its only output with all 4 pins), and ignore all the others' (by omitting Pin #3 is the "other" outputs). This has NO impact on ability to control fan speeds. ALL fans on that Splitter receive the same signals. However, since your fans are different models, they will run a different speeds.
Your problem, though, is not different speeds. It is NOT running for the Noctuas.
The mobo manual is not fully informative. It has three SYS_FAN headers, but the last one (SYS_FAN3) can do NO speed control - it can only provide full power (and hence constant full speed) to a fan. SYS_FAN1 and 2 both have pinout labels that say "VCC" for Pin 4, and "12 V / Speed Control" for Pin #2. Now, a 3-pin older fan header using Voltage Control Mode would provide on Pin #2 a Voltage ranging from 12 VDC for full speed down to 5 VDC for minimum speed without stalling. Of course, with no Pin #4 it provides no PWM signal. On a true 4-pin header that IS using the new PWM Mode, the voltage on Pin #2 is always 12 VDC; then the PWM signal on Pin #4 is used on a 4-pin PWM-design fan motor by a special chip that modifies the flow of current from Pin #2 though the windings to alter its speed.
The design of the new PWM 4-pin fans has a few backwards compatibility features. One of them is this: If you plug one into an older 3-pin fan header using only Voltage Control Mode, it gets NO PWM signal so its chip cannot modify current flow. HOWEVER, the power on Pin #2 is a VARYING Voltage, so the fan speed IS controlled in this situation. In some earlier mobos as this fan type was introduced, the mobo used all 4-pin fan headers BUT only used them like 3-pin older headers and did NOT provide a PWM signal on Pin #4. This made such headers "universal" because they could control the speed of EITHER type or fan. So we can consider the question: is YOUR mobo this type that uses only the older Voltage Control Mode? The fact that ONE part of the label for those headers says "Speed Control" suggests that may be exactly what it is doing but we cannot be sure from the labels.
Suppose for a moment that they ARE operating as older Voltage Control Mode headers. If that is the case, it is POSSIBLE to supply to a fan a Voltage that is too low to start it up, and it will not start until the voltage is raised. Exactly what the minimum Voltage is to start the fan will differ from one model to another, so what DOES start one fan may not start up another. MAYBE that's what you are seeing.
BUT, how does that come about? IF you are using the "Normal" Profile (see your mobo manual p. 23), the standard action of a mobo at start up is to turn on ALL the fans at full speed for a few seconds to be SURE they start up, then reduce that to a lower Voltage according to the cool temperatures of a recently-started system. LATER it will raise the voltage to raise fan speed as your system warms up.
However, what if you choose the Manual Profile, which allows you to specify a fixed fan speed for all conditions, without any automatic changes for temperatures? You might set it so low (trying to be quiet) that the one fan can just start up, and the others cannot.
Another possibility is hinted at on p. 23 under the "Normal" setting - it says "You can adjust the fan speed with Easy Tune ..." This sounds like you can use their Easy Tune Utility to make your own settings of what speed the fan should run for what measured temperatures - a feature called "Custom Fan Curve" in more recent mobos. In that scenario you may have the option to set the minimum speed for a cold system, and then higher speeds for hotter. IF you have that, yours may be set now so that the fans all DO start up at boot time, but then settle down to a very low speed - so low that only the Arctic fan can keep going, and the two Noctuas stall. LATER as the temperatures rise and the control system increases the Voltage signals, eventually you get a Voltage high enough to re-start the Noctuas, and they will stay running until the system cools off a lot. SO, try this. Go into Easy Tune and examine the settings for the lowest temperatures and fan speeds. Change the lowest fan speed setting to something higher. That may well prevent the Noctuas from stalling right after start-up so they work all the time.
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