I am just now (finally) starting on my first home built machine, mostly from the current Ars Hot Rod. I have a Gigabyte GA-7DXR mobo & a Super Micro SC750-A case (the thing's almost as big as some ...

I think you just can't read right. Those manuals are always confusing, though. I have never had a case (no pun intended) where I didn't have these problems.