Fan speed issue after installing Command Control on Windows 8.1 x64

Specs:

Windows 8.1 x64
Intel X58-based Alienware Aurora mobo
12GB ram
Intel i7 920

I'm not sure which Aurora version I have - it's from 2009.

My problem:

I've installed Alienware Command Control software to tweak the loudness of my fans (specifically to stop the pci fan blasting to full speed at modest cpu loads during gaming) - I used the Thermal Control settings within CC to manually set a curve for what speeds fan should be at for a particular temp.

I saved those changes then went back to Auto control to contrast and now my pci/hdd fan are constantly at full blast.

What have I tried:

I've fiddled about with the curves including trying to move to a manual fixed speed. I've switched back to auto. I've tried making these changes then rebooting. No dice.

I've uninstalled/reinstalled the CC software (including removing leftover reg entries/directories). No dice.

Curiously, if I install the software and reboot, the fan speeds are fine. Right up until I reboot again whereupon they go at full speed again.

I've reset the MIO board by;

Draining power by unplugging from mains and holding the power button down for 30 seconds, leaving for 30 seconds then replugging into mains.
That didn't work.

I've disconnected the fans and powered up the pc to windows then shutdown. That did nothing.

I've switched the "Factory defaults" jumper to reset the MIO to defaults. That did not work.

I've removed the CMOS battery for 10 mins then reinserted and booted up. That seemed to work because whilst I was reconfiguring the BIOS again (none of the settings have anything to do with fan speeds btw) the fan speeds were normal. But once I save the BIOS and reboot, the fans go back to being mental little devils.

So, after some googling, it seems like the issue could be that the CC software has upgraded my MIO board to a firmware version which is incompatible with Windows 8.1. The software itself is something I've used a lot but only ever on Windows 7 x64 systems. There was no indication it was not compatible with Windows 8.1 x64.

I ran the ePSA thing in F12 menu and it found no issues. I don't have the Dell Diagnostics CD anymore.

I have a few questions before I buy a replacement MIO board

1. Will downgrading then re-upgrading BIOS do anything (if even possible)?
2. How can I be sure that, after CMOS reset, I'm not recovering previous BIOS settings? BIOS A11 introduced this facility. I'm curious about why the fans seem ok after cmos reset until I have entered and saved BIOS.
3. How do I properly reset the MIO board (if the above doesn't do that)?