It was very sensitive to slight shifts in the signal phase
That's the whole idea! Basically you're working out the phase angle of the signal with respect to a fixed sine wave of the same frequency.
I've found that some motors are noisy and some aren't. It also depends on the prop - or in my case the ducted fan which is a whole lot more succeptable to accoustic ringing due to low freq pwm. In serious motor controllers the DSP's use a slightly varying pwm freq to avoid any chance of audible noise.
This is a great thread, BTW!