Old thread, yeah, but I've had similar problems with a Rampage VI Extreme Omega. My fans were blasting even, right out of control and nothing seemed to get Fan Xpert to work properly. Hence, I uninstalled AI Suite, and then did Windows reinstall via Windows "Settings > Recovery." After that I did not reinstall AI Suite or Armoury Crate or any of that kind of thing (more like bloatware, really, and that can even still be active once uninstalled--which is why a Windows reinstall is needed). Fans can be controlled via the Bios and as I found with an earlier Rampage III Black Edition motherboard, that is by far the best way to do it and how to once and for all rid yourself of a lot of headaches now, and down the road.
Figuring out how to control the fans via the Bios might require some research, but it is worth it. I'd also recommend monitoring your core CPU temperature & GPU temperatures, etc. via HWMonitor as well, just to be sure your fan settings are the best ones.