I just ran into this problem. My 980, while full load, has only 1 fan spinning. Even at 90 degree Celsius (running fumark stress test). I have turn on the gaming mode and turn off Zero Frozr on MSI Gaming App. So I thought 1 of my fan just not working. But this is what I don't understand, when I use Cooler boost on the app, both fan run at 100%. Is this a driver issue?