I recently installed an Arctic F9 intake fan in the front of my case, and attached it to a PWM 4 pin connector on my motherboard. BIOS initially reported that it wasn't running but when I examined the fan it was clearly spinning. SpeedFan and CPUID also only register 2/3 fans.
Should this be a concern? I'm hoping that it's not equipped properly with an RPM sensor, and BIOS is still regulating its speed accordingly.