I replaced the motherboard in a friends computer with a X58 Classified 3.  And am replacing Vista x64 with Win7 x64.  It has a MSI N260GTX NVIDIA video card which worked fine in Vista.  Upon installing Win7, the install would quit and hang in the very final stages of installing every time.  In order to complete a install I had to remove the card and put in a Asus Radeon HD6570 card I have.  Once I had Win7 installed I put the NVIDIA card back in.  It would boot fine with Win7s generic VGA driver, but as soon as I would install any NVIDIA driver Win7 would hang on startup at the colored orb windows flag screen.  I tried every version available NVIDIA and MSI/NVIDIA and the Windows update NVIDIA drivers with the card and none of them would work.  I also tried various BIOS configurations.  And with the v82 BIOS that came with the motherboard and the updated v83 BIOS. 
 
Finally I moved the card to the second PCIE slot, and it worked fine with the NVIDIA drivers installed.  Now normally I would say, "ok the first slot is bad", but the Radeon card works just fine in the first PCIE slot.
 
Which brings me to my question.  Is the first slot actually bad, or is there some kind of BIOS problem that has yet to be fixed that keeps the NVIDIA card from working in the first PCIE slot when NVIDIA drivers are installed?
 
Now let me add to this that the internet is rife with people having problems with various NVIDIA cards combined with various motherboards, combined with Win7 hanging when installing and/or starting up Win7.

It's not a card problem it's an old bug in Windows 7 that deals with memory which was fixed in SP1. Just repeat the install using one stick of ram and that should work. After the install install the other sticks.

Now this is a SP1 install of Win7.  I installed it using two sticks of RAM, but installing with just one stick will make a difference?

Nope, that didn't work.  With one stick of RAM the install hangs and wouldn't finish just like before.

No, but it would appear to be a problem related to the Classified 3 motherboard with NVIDIA video cards when seated into the first PCI-E slot. This seems to be happening with recently manufactured models, for some strange reason. 
 
Others, including myself have experienced this problem. I have personally went through two Classified 3 motherboards, which both had the same issue with my GTX 570. For the most part the video card works fine in the 2nd, 3rd and 4th PCI-E slots, just not the first. I also tested two GTX 570's and a Radeon HD 5870 which worked fine in the first slot, however none of the NVIDIA cards worked. 
 
I am actually running on another motherboard with my video card in the first slot without an issue. 
 
 

I have two E770s, one not so new and one just about a month old.  I have both Radeon 6950s and GTX 570s, never had any issue with the first slot working properly.
 
Could it possibly be something done during installation?, what version of BIOS did your board come with?