Because something is setting a minimum of 1000 rpm and Afterburner can't override that. The PWM signal is always at 29% but it doesn't matter if it is a 5000rpm fan or a 1200rpm fan, it will idle at 1000rpm. I can connect a 5000rpm fan and then feed the PWM signal to a 2500rpm fan and then it will spin at 500rpm. But if i connect it directly, it will not go under 1000rpm.
Because I got a really good deal on a Palit GamingPro but I would like it to be 100% silent, and my ThermalRight HR-03 can do that, if I could just control the Fan. I could make a fake tach signal generator to make it work, but I would rather hack the Nvidia Driver if that is the reason for the 1000rpm minimum issue.