You stopped the cpu cooler's fan and it carried on. Bear with meon this one:
PWM is not a DC signal, it's a signal that rises to full voltage then back down to zero at a high frequency, within audible range. Stopping the fan won't necessarily stop the buzz cos the pwm signal will still make the fan's internals vibrate. It stops, you open programs increasing the load on the cpu, increasing the temp, thus increasing the fans speed via a stronger PWM signal.
I'm not that familiar with your motherboard but can you go into the bios. I'm working from my mobo's manual here, maybe a section 'PC Health Status', then maybe 'CPU Smart Fan Mode'. If it's 'PWM' or 'Auto' change it to 'Voltage', save and reboot. See how that goes, will eliminate the fan at least.