[BUG] PWM Fans are noisy

[SirRonBird]

Description

Both of the PWM controlled Fans are quite noisy, by that i mean there is this typical pwm noise.
I use the original Ender 3 electronic-case-fan and as the part-cooling-fan a DC 12V/24V 2 Pin fan. Both are directly connected on the board.
I use the precompiled firmware-bltouch.bin.

Expected behavior
Fans should be much quiter

Actual behavior
they aren´t quite

[DanielYWoo]

the board fan is very noise when pwm is from 4% to 99%, same here.
But finally I realized that the SKR mini e3 board swapped the part cooling fan and the board fan....
@SirRonBird try swap the fan.

[thegwydd]

I have the same issue.
@DanielYWoo, can you explain better what you mean by "swap the fan"? In my case the part cooling fan is connected to the proper connector as I can drive it using marlin menu.
Are you talking about Vcc and Gnd?
I've just double checked my connections with the schematic and Vcc and Gnd are correct.

[DanielYWoo]

@thegwydd No. I am NOT saying VCC/GND swap. You can check the SKR mini E3 schematic, the layout of the two fan connectors are different from the stock board.