It is the weirdest thing that I have ever encountered.
Couple of days before I ordered the Maximus VII Gene motherboard, I ordered the Silverstone Heligon HE01 CPU cooler. The cooler worked pretty well on my old Maximus VI Hero motherboard. I had the fan on the CPU fan header and just used the automatic fan control settings in the UEFI.
But when I installed the cooler on the new motherboard, the fan stopped working properly. When I say "stopped working properly", I mean that the fan did not want to rev past 500RPM. The fan is supposed to rev up to 2000RPM at its maximum PWM signal strength. What's so special about 500RPM figure is that it is the lowest RPM that the fan can operate using the PWM signal.
I blamed the motherboard at first. That was the obvious thing to do given the circumstances. I thought the PWM signal from the motherboard was not compatible with the fan. Asus does a lot of non-standard things with their motherboards (that's to give more value additions of course), the Fan Xpert feature in this case.