vortex681

But you're not comparing like for like. That was the fastest speed PCIe 2.0 slot (x16) compared to the slowest speed PCIe 1.0a slot (x4) - of course there'll be a huge difference. A better comparison would be to put the same card in the same speed slot in both types of PCIe bus. From the final table in your second link, 1920x1200 at more representative settings, the 8800 GTS in PCIe 2.0 x16 gave 27.9 FPS. The same card in the PCIe 1.0a x16 gave 25.9 FPS - that's only 2 FPS difference. If the PCIe 1.0a slot was seriously bottlenecked, you'd expect a much larger improvement when you changed to a PCIe 2.0 slot, and that's not the case.
 
The point that I was making earlier is that if you want to buy a PCIe 3.0 card and run it in a PCIe 2.0 x16 slot until you upgrade your motherboard, there won't be much of a difference in performance in FSX (or most games, come to that).

Just restarted FSX (for the fourth time) to try to figure out what could be causing the problem and all of the buildings are back! Didn't change anything in the mean time so no idea what caused it. I think it will remain a mystery.