Not to my knowledge, ntune shouldn't cause that. I mean, you've gone as far as a clean install, that would take care of anything third party wise that would oc your card. My only other suggestion would be to dl a fresh bios and flash it. mvtech
has everything you would need.
I've never heard of this problem on any card before, so flashing it is just a suggestion. I'm sure you've googled and searched the manufacturers web site to see if any others had this.
Good luck with it.