Mate I have exactly the same issue but on Asrock X99 Extreme4.. It happens exactly the same thing. When chassis fans spin at lower than 1000 rpm, the readings are correct and only go +-20. If I set them to spin higher than 1000 rpm the programs (all of them including bios readings) start reading spikes. The most usual spikes are either 0, +1000 than normal (for example 2130 instead of 1130), or 19640.
I want to underline some things. I have 3 chassis fans that came with my case (Zalman R1). I have plugged the back fan on the Power Fan slot of the mobo and the 2 other fans on chassis fan 2 and chassis fan 3 slots of the mobo. The false speed readings occur ONLY for the fans that are plagged on chassis fan 2 and 3 slots. The one that is on the Power fan slow readings are always correct with no strange spikes.
At this point I have a question which is the only thing I can think of that MAY have cause any dmg to the sensors. When I installed my mobo I did apply some pressure cause I had forgotten to put the very right side of the mobo standoffs. So as the right side of the mobo was hanging in the air (about 5 cm of mobo panel width in the air), the mobo did bent when I was plugging the ATX PSU cable for example which goes to the very far right side of the mobo.. So if that bent might have caused any problem to the sensonrs... But again, would it harm ALL the sensors? How possible is this? The 2 fan slots I use are not even close to each other.
So just in case I'd like to ask you if you "mistreated" your mobo when placing it in any way like the one I mentionted without being sure that it could cause such a problem. Also you said your fan 1 and 3 have this behaviour.. Do you have any fan plugged on slot 2 which works fine or you don't have any fan there that's why you didn't mention it? Other than that our problems are identical so I don't understand why you think it is mobo specific problem. If you found any fix I'd like you to share with me.
