I'm intrigued. Starting point is this: you can control the speed of an older 3-pin fan ONLY by varying the Voltage supplied to it from Pin #2 of the header. Control of a newer 4-pin PWM fan's speed is done differently. So you cannot MIX those two types on ONE mobo fan header because they require different types of signals.
Now, you say these two actually ARE on different headers. Good! Next, I see from the mobo manual that there is NO mention of this matter of different header signal types. The manual shows 4-pin headers labelled as PWM Mode only, which suggest that it can NOT control the speed of a 3-pin fan. Such a fan should run full speed all the time. HOWEVER, your post also says, "When the non pwm is at its most effective rpm ...", suggesting that somehow you have been able to adjust its speed. HOW?
MANY modern mobos have a configuration option for each header that allows you to specify whether it behaves as an older 3-pin header in Voltage Control Mode (aka DC Mode), or as a new 4-pin header in PWM Mode. When you separate fan types onto different headers, then you use this feature to set the header for 3-pin fans to use Voltage Control Mode, and the other header for 4-pin fans to PWM Mode. Although the manual does not say you have this, is that feature actually there? Is that how you control the speed of the 3-pin fan? If yes, then just ensure each header is set this way.
If I read your first post correctly, you have only TWO fans you are concerned about, and each is on its own mobo header. You do NOT mention having a Fan Hub or a Splitter involved in any connection from fan to mobo. Is that right?