Nothing to do with Mach3.
It is the current mode operation of the driver.
Live with the noise, or reduce the supply voltage, and lose some top end speed.
This occurs when the chopping does cycle skipping, because the minimum pulse width won't go any lower.
Don't confuse that minimum pulse width with Mach3.
It is a function of the driver, the stepper motor inductance, current setting and supply voltage.
If the motor,driver and power supply can take it, increasing the current setting may quieten it.
Turning off current reduction when stopped might also stop it.
Hitting the reset on Mach3 won't help. You will just lose your reference if microstepping is used.
Super X3. 3600rpm. Sheridan 6"x24" Lathe + more. Three ways to fix things: The right way, the other way, and maybe your way, which is possibly a faster wrong way.