What motherboard do you have? I'm not 100% sure on this, but it might be because of the PCI-E's electrical design on the board (1 GPU on PCI-E x16 and the other might be on x4 (even though it's an x16 slot)).
Like I said, I'm not sure.
Wow...I'm at loss. There was indeed people who had issues with it, but they claim it's either the SLI bridge that could be screwed up or the board has a problem.
For the sake of just trying, if you have a spare HDD lying around, try a fresh install on it and try out SLI with it.
I hope it's the SLI bridge, because pretty much the only thing I haven't tried is getting a new bridge. Otherwise I was thinking that the 2nd PCI slot could potentially not be working correctly.
