Aurora-R4, 8.1 update, Fan Issues

My PCI and Hard drive fans just started running wide open all the time shortly after Windows 8.1 update. They respond to manual control but when on auto they run at 100%. I uninstalled the Command Center Controls, removed the registry keys, rebooted and installed the latest Command Center package from the web and the problem persisted. Thinking it was a Windows 8.1 error I reset to the factory Windows 7 build that originally came on the computer and it seemed to work correctly for a day or so and is now running the fans wide open again. The ePSA diagnostics check out and all the fans past diagnostic testing. All temperature readings say 77 degrees F and it states the cooling pump is running. I'm seeing alot of info about faulty  master I/O boards possibly being the culprit. Anyone have any experience with this issue before I jump through tech support. I work overnights and can't troubleshoot on the phone with a rep until next week.

Aurora R4

I7 3930k

16gb Ram

GTX 660

Intel SSD boot drive

Running updated A09 Bios from the support site and now have Windows 8.1 64Bit back on the system