I don't know the technical specifics as to why this happens, but it can be related to the "start" voltage of the fan.
Tell us what fan you're using.
Some mobo software "might" enable a fan-control function, but the ASUS software for my boards isn't that sophisticated. I've had very good and reliable results with SpeedFan. There are some advanced settings which may change the way SF controls the fan.
There is a threshold below which SF is unable to keep the fan speed where you want it, and I think this has to do with the fan specs.
I have a Delta Tri-Blade 120x38mm on my CPU cooler. I've been trying to reduce noise even further (it's already a whisper) -- and I was experimenting with the settings. When I drop the minimum speed setting down below some 46% of "full" -- the same thing happens with mine which happens with yours. I'm sure it has to do with "start" voltage, or the fan-motor's capabilities.
You'd have to look into it more -- I'd appreciate being "corrected" here in this thread, also -- but SF uses "PWM" or "pulse-width-modulation" for fan-speed control. I do not think it changes the voltage going to the fan, but varies the continuity of the power.
It seems I might be contradicting myself in this post, so I hope my remarks are helpful, anyway.