I understand your logic, and certainly appreciate your point of view providing assistance in a support forum where you have little idea of the environment, and more importantly, the user. You are saying it's not proven to be broken. I agree with you. In fact I hope there is something simple that will fix it. PEBCAK would be ideal for me. I am merely saying that unless you already know the problem it is premature to state the board works just fine.
Anyway. Moving on. I appreciate you helping.
I am using 5 Gelid Silent 12 PWM fans (
http://www.gelidsolutions.com/products/index.php?lid=2&cid=5&id=30 ). The are 4 pin fans, obviously.
They are directly connected to the 5 on board fan controllers.
I have tried with several different fan bios settings. But I think the easiest one to demonstrate the issue will be when set to "silent" control in the bios.
Here is a sequence of bios shots. I could not use the print screen function as it merely popped up a window saying select the USB flash drive but gave no options to select, despite me using the same USB flash drive that worked to udate the bios firmware. (I tried two different flash drives... is there a trick to getting screenshots to work like this?)
Rebooted into bios. Fan control was disabled and so all fans were running at max speed. Here are shots of the fan monitor, the fan control settings, and then how I changed those settings to enable fan control to the silent setting.



*reboot*
Now here is the fan monitor after the reboot. Note only CHA FAN 3 is being set to a slower speed, while CHA FAN 1 and CHA FAN 2 are running at max speed. CPU FAN and CPU OPT are also running at slower speeds. CPU and Board temps included. And then how I changed the settings to manual.



*reboot*
With the manual settings, note the fan monitor speeds again.

*shutdown*
I then moved the fans around. C1 fan moved to C3. C3 fan moved to C2. C2 fan moved to C1.
*boot*
Note that now the fan that was previously on C3 and being set to a slower speed is now on C2 and is running at max speed. Conversely, the fan that was previously on C1 and running at max speed is now on C3 and running at a slower speed.
This is consistent with the noise and visual speed at which the fans are moving. ie, it is not an error in the fan's RPM signal. It also strongly supports that it is not the fan's PWM controller.

At no time did I enter windows during this test. If you would like me to install any software and report on software tests i will gladly do so on the clean install I have.