This is what "I" would do... your miles may vary!
Get the latest software from MSI... chipset drivers and latest Bios.
Latest Realtek drivers for Audio... Same thing from Nvidia
I would unplug everything from the Mobo that does not need to be there for new OS install... I would leave 1 HDD (the one where the OS will go in of course), 1 CD/DVD Rom and if the CPU comes in with onboard graphics, I would even unplug the GTX660. I would even pull one of the RAM sticks just for good measure. Last but not least, make sure you return your mobo to its default state.
Now, start with the Windows CD and make sure you do a clean install, better if you format the drive while you at it to avoid any old remnants, once you are done with the windows OS, install the chipset and if you can update your Bios, why not. Do the same with the Audio and Video drivers.
I would then try to play that game you are having issues with to see if all is well... if it passes seat of the pants reviews, then go ahead and finish plugging in all of the other devices that you unplugged before.
I know, this is just insanely annoying and I only do this as a last result but, the way I see it, because of the fact that you have installed a new OS on top of a corrupt OS you may be having this issue or it just may bad luck... all I know is that there have been times when nothing wants to work and I have had to remove everything and I mean EVERYTHING and start all over again. Perhaps because of my lack of knowledge of computers I am having to go the extreme way but it sure seems like you have nothing to loose but time at this point!
