What fans are using mate?
In all the time I've built these things, and we are going into the dozens of units and two years here, I've never heard a pop from them. Don't get me wrong I've blown transistors, had smoking potentiometers, scalding hot resistors and transistors but I've never had any audible feedback from the components.
I've seen fluctuating readings before but that's generally when the speed, and corresponding voltage, of the fan drops below around 4v or 5v and therefore leaving the PWM signal stronger, so the motherboard picks that up instead.
I've not really tested with PWM quite as low as 15%, it's generally designed for 30%+ PWM. I've never stated this because in a lot of cases you aren't able to go quite that low with PWM duty cycle.