I have the GIGABYTE 990XA-UD7 its a very nice board will handle 6 gpus running @ 4x and a pci card. I think your problem here is you are using two power supply. Computer power supply have to be rated specifically to be uses in pairs. There has to be internal isolation between rails and grounds otherwise you can get up to 24v on a rail. Thats most likely why it died. Modern graphics cards only pull signal voltages off the cards. There is not enough current draw though the board to kill it, its the voltage. The reason risers work is when somebody uses power risers it usually power by the same supply. Also if you do not provide enough power under voltage can kill a card or motherboard as well.
Since you rezzed this old thread, I thought I'd bring this part up.
I'm using those PCIe USB powered risers. I have multiple setups where a riser is being powered from a different PSU than what is powering the GPU itself.
We're using Rosewill Capstone 750W Modular 80Plus GOLD. Every rig has two of the same PSU.
So how are our rigs still working just fine, if you're saying this could cause problems?
Also, how on earth could we end up with 24V on a rail, coursing through the GPU? Or the motherboard for that matter? If we were to somehow get a 24V draw, something else would be wrong than the inherent design of the rig, and I doubt we would even be mining right now.
I'm legitimately curious, as I know a lot of people run multiple GPUs per rig, and we're doing it on multiple rigs with no issues. Is it because they're the same make/model of PSU that it's fine?