MORE Food (info) please. Make and model of MB. I'm assuming you have a x16 GPU card.
The P55/P55A for example.
If you have 2 gpus installed, both X16 slots will operate @ X8
Also if you plug an X4, or X8 addin card into slot 2, both slots will be X8. My ATI 5770 was @ x16, but I then added the Asus U3S6 card in the 2nd X16 slot, Slot 1 (GPU) was downsized to X8.
For P55A (at least some) if you enable the USB3/Sata 6 option in BIOS, the two X16 slots become 2 X8 Slots.