The Smackover board is supposedly notorious for being a problem motherboard I've learned through this experience. I have five copies of this specific board - each of them behaved in an identical manner. In my case it was definitely the board, not the GPU. It seems to me like this is most likely true for your case as well.
This does not rule out the possibility for the issue to be fixed by a BIOS update on the GPU, however. Such was the case for me and my 780. Make noise about it on your GPU manufacturer's forum, that's what I did. It worked. 
After contacting Intel support about a potential BIOS upgrade, I was told that they have no plans to upgrade it for the DX58SO, DX58SO2, DX68BC, or DX79SI.
I know that really blows for you having to deal with that inconvenience of having both cards on the motherboard sucking power, but to me it seems like your best option is to go the route of trying to get a GPU BIOS update rather than one provided by Intel to the DX58SO.
I'll also not be investing in Intel motherboards in the future from this experience and with Intel's support for this issue. (Although it's not their support team's fault for not being able to solve this, it's their engineering team or whatever team decides polices about EOL board support)