Check the manual. I believe you have to use a specific slot for a single GPU configuration, and i've believe most use the 2nd, not the first slot; most of the time making the first PCI slot un-usable . .
+1 My roommate has a eVGA mobo and he can't use the top most slot for a single video card, he has to use the middle one, or course this was after several hours of dicking around till we read the manual.
It's fine dude, just deal with it.