I've got a bit of an interesting problem. Just built a new rig, running a Gigabyte GA-Z77MX-D3H mobo, and bought a HIS HD7850 to go with it.
If the graphics card is plugged into the 16x or the 8x PCIe slots, the whole computer gets bogged down, takes about 30 seconds to get to the BIOS splash screen (which it loads in slow downward waves), and then ages more to get into Windows. The graphics are then generally laggy once in windows (ghosting, input lag, etc). None of these problems happen while the card is in the 4x slot (pc boots in seconds, no lag, all that healthy computer stuff).
The interesting bit is I've got a second card (HD6770) lying around in my old rig. I tried putting it in the 16x, 8x and the 4x of the new rig, and the computer worked perfectly wherever I put it. Likewise, the 7850 works perfectly fine in the 16x slot of my old rig.
I RMA'd the 7850 (as that was my first guess to the problem before all this testing of slots), but it has no issues.
Rest of the pc specs: 750W PSU, i5 3.4ghz quad core, 8GB RAM. I was originally running BIOS F5, upgraded to F8 to see if it made a difference (it did not).
Anyone got any ideas where the problem might be? I'm not sure where to go from here, since apparently everything works fine in isolation.
Conclusion came to: The 7850 is a PCIE 3.0 card, and the motherboard runs PCIE 3.0 on the 16x and 8x slots, but not the 4. The 6770 works in all those slots because it's PCIE 2.0, but stick a 3.0 card in a 3.0 slot, and stuff goes wrong!