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PCI-e x16 slot showing as x1 in speccy

I just purchased a refurbed MSI motherboard for its SLI capability, and it seems that the second PCI-e slot is having issues. Device Manager and Nvidia control panel can't see the video card in slot 2. Both cards work when in slot 1, but neither shows up in the other one. Speccy shows that PCI slot as present, but running at x1. Here's the weird part: I've tried everything from uninstalling the drivers with DDU to reinstalling Windows, and the only time I have ever seen both cards listed was in the DDU removal tool in safe mode. Is there a setting I can tweak to get the second PCI slot to report correctly, or is this refurb just no good? I've ordered another mobo, but I can still cancel that order if I can get this one working.

I appreciate any advice.

btw, here are my specs:

MSI 990fxa gd64 motherboard
AMD Phenom II X6 1090t CPU
8 gigs DDR3 RAM @533 MHz
EVGA Nvidia GTX 460
MSI Nvidia GTX 460
Windows 7 Ultimate
Rosewill 950w PSU
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  1. Best answer
    1) Update the BIOS ( it should be the 990fxa gd65 ). http://www.msi.com/support/mb/990FXA-GD65.html#support-cpu
    2) Update the AMD chipset driver too, the chipset driver comes with the pcie controller driver, that will make sure there is not the driver problem. http://support.amd.com/en-us/download/chipset?os=Windows%208%20-%2032

    After that, if the pciex16 still shows as x1 under load, because the gpu may run power saving mode in idle, you may try use the cpu-z too. Otherwise the MB has problem.
  2. Speccy is wrong on things sometimes, including PCIe slots on Dells and HPs. It will often see a PCIe x16 slot as "Proprietary" and only x1 lane. But it's wrong. Doesn't mean your mobo is failing. Don't take speccy's info as authoritative. It's far from it.
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