My BIOS shows this http://www.ryderocz.info/evga680i/680ievga8500sli6.jpg (not my picture, but mine has the exact same thing)
Two bottom cores are greyed out.
Two bottom cores are greyed out.
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It almost sounds like you don't have enough clamping pressure holding the heatsink in place. The mounting bracket in the link you showed is for a socket 1366 / i7. The pics of the 775 bracket look a bit different. Perhaps they have a different bracket height. This link is to the brackets for a socket 775 mb - http://www.thermalright.com/new_a_page/product_images/cpu_cooler/ultra-120_extreme/revc/10.jpg