Any monitoring tools being run on the system?
No, nothing. Its a fresh install of Windows (it was doing it in 8.1 and now I'm on 10). Its hard to describe, for example as I scrolled down this page, each time I turn the scroll wheel all the fan spin up and slow down. The fans seem to be reacting to everything even though the CPU temp is a constant 24*C.
I went ahead and bought a brand new set of fans to try out, maybe one of them is bad and causing the controller to have issues? They're all PWM Noctuas I've had for a long time.
EDIT: removing the water loop and all of the fans I used and switching to my air cooler with completely new corsair fans and re-running the q-fan tuner seems to have fixed it. One of those fans must be faulty, or the pump.