Try to update the BIOS, and intel chipset driver first, then try again. If you get the same problems, nothing you can do.
And if you can still use the 2nd pcie slot, you should be fine, read the review, even it is old, but it will tell you something at least.
Many hardware sites have shown in the past that video cards do not show any performance decrease by running in x8 mode and cannot utilize the larger bandwidth provided by the latest Gen3 specification. However, video cards are getting faster and faster so we felt it this is still true. Also...
www.pugetsystems.com