You are not the first person to have this issue. I have never been able to get the CPU Fan 1 speed with a PWM fan below ~1100 RPM. I've used fans rated at 500 - 2000 RPM, with the same result. It seems that the lowest speed a PWM fan is allowed to run at on the CPU Fan 1 header is ~1000 RPM.
A different board manufactures fan speed control software I've used has a calibrate feature for the PWM fan header. It checks the fan's speed with different voltages, and uses that information to set the fan speed. A line graph profile is used to define fan speed in % versus CPU temperature. But this method is not fool proof if the fan is changed and not calibrated. The board also has low fan speed warnings, which covers that problem.
I doubt there is anything you can do about this. Using the chassis fan headers with manual control, I have gotten fans down to ~500 RPM. Manual CPU fan speed control is ridiculous, so not a solution. Changing fans won't help either, unless you can find a 120mm fan that is very quiet at 1000 RPM, when mounted to your cooler.



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