Since the two fans on your CPU cooler are of different designs, there is a detail you should check. The basis of this is that a THREE-pin fan connected to a header using the new 4-pin PWM Mode for control will always run at full speed, whereas a 4-pin fan's speed WILL be controlled in that scenario. So, start by setting the configuration of the CPU_FAN header as I said above - especially using the Standard Profile setting. That will have the header try to control the fans' speeds.
Start with your system cold after NOT running for a few hours. Now, open the case so you can observe the two fans carefully. Reboot and watch those two fans immediately. For each of them, the normal sequence is that they start up at full speed almost immediately, but after a few seconds as the boot process is nearly complete, they both should slow down to a low-speed setting suitable for a cold system. NOTE what the fan speed number is.
For the next test, reboot directly into BIOS Setup and go to the CPU_FAN header. Set the Profile to Turbo, back out and go through the Exit Menu to Save and Reset. Again, watch the two fans. This time they should start at full speed and stay that way at all times. NOTE the fan speed shown this time.
Next, reboot into BIOS Setup and change the CPU_FAN profile to Quiet, then back out and reboot. This time BOTH fans should start at full speed and the BOTH slow down a lot. Note the new Fan Speed.
If there is difficulty in deciding how fast the two fans are running, you can re-do this test series but with one fan (say, the added 4-pin fan) disconnected from the Splitter so that you can concentrate on only one connected fan. Then do it again with that one re-connected and the OTHER fan disconnected.
If all those tests show that BOTH fans change from fast so slow when they are supposed to, then your fan control system IS working. If they show that ONLY the 4-pin fan's speed changes but the 3-pin fan never gets to run slow, then we have an answer. Such behaviour would tell us that the header is using ONLY the PWM signal system and it can NOT change the speed of the 3-pin fan, no matter how you set the Profile for the header. The sound that one fan makes may deceive you into thinking that neither fan's speed is under control.
Report what you find back here. There are a few options for what to do next, including leaving it alone. We can discuss when we know what those tests show.