Why are PCI-E slots not configured correctly (X58 board x16 at x8)

Hi. I apologize for this first paragraph but I am not sure at this point what may be relevant. I have a Gigabyte EX58 Extreme motherboard with a Core i7 965, Twin BFG Geforce 275 GTX OC in SLI, and 8gb of DDR3-10,200 memory running at 1333 @ 1.7v. Power supply is a Corsair HX1000W dual rail and I had the same issue with an Ultra X3 1,600w. I am not sure if all of this is relevant to my question but they may be. My Northbridge is listed under Everest (on Core i7's the NB controls the PCI-E slots) as: Intel Tylersburg X58. All my PCI and PCI-E slots I only have hardware in the PCIEX16_1 and PCIEX16_2 slots (the board has two PCI-e 2.0 x16 slots, plus a x8 for 3-way SLI and which shares bandwith or whatever with the second x16 slot which causes it to run at x8 also). Finally heat is NOT an issue as this board comes with a waterblock on the Northbridge which I am cooling with a Coolit Freezone Elite chilled coolant system, CPU is phase change (modded Promethia Mach II) but I am stil waiting for good aftermarket coolers for the 275 GTX's so they run at 85% fan (although I have two fans dedicated to directing heat away from the cards and they never exceed 50c. The problem I am having is not due to overclocking as I have all settings default. ADDITIONALLY, I just replaced an Asus P6T (a temp for a busted Rampage) which GAVE ME THE SAME PROBLEM. I have flashed to the latest BIOS and am running the latest drivers. My OS is Windows 7 64bit. Also please don't ask if I know if the cards are in the correct PCI-E slots.

Sorry for the long intro but I really do not know what is relevant as I have been seaching for a resolution for awhile. The question is simply this: Why with the above specs when I run two BFG 275 OC GTX's in SLI in the two PCI Express x16 slots they run at x8/x8 IN BOTH SLOTS instead of x16/x16? I have confirmed this with GPU-Z as well as with Everest which says both cards are in PCI-e 2.0 x16 slots but shows them both running at x8 (in bus 2 and bus 3 according to Everest which later identifies bus 3 and bus 7 as the PCI-e x16 ports). I read somewhere about IRQ assingments possibly being an issue but it was vague. Finally I do not think a particular card is the problem as I have three 275 GTX's OC (I was going to run 3-way SLI but as usual the bottom card destroys any wires in your USB slots, case connectors etc. and on many cases no fan output) I also forgot running in the x16 and x8 slots cause the top PCIEX16_1 to run at x8 and the bottom PCI-e x8 to run at x4. I would greatly appreciate any suggestions. Thanks in advance.
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  1. It's possible that the motherboard can't run two cards at x16/x16? Have you checked the specs thoroughly?
  2. The motherboard is a Gigabyte EX58 Extreme designed to run two cards at x16 and one at x8. By the way I cannot believe I left out my power supply is a Corsair HX1000W and I had the same problem with an Ultra X3 1,600w. Thanks
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