Is a MacPro3,1 (2008) x16 slot PCIe 2.0 or 1.1? On a 2008 Mac Pro (a.k.a. MacPro3,1), it apparently has 2 PCIe 2.0 slots and 2 PCIe 1.1 slots. While the difference won't prevent any PCIe device from working, it does make a difference for speed.

I recently ran GPU-Z under Windows 7 and ran the load test (a '?' icon off to the right next to text about PCIe versions and number of lanes) and found that it stayed at PCIe 1.1 x16. This is with a Radeon HD 270X which is definitely PCIe 3.0 compatible, so I'm a bit surprised it didn't report 2.0!

Trying to look at Intel 5400 chipset documentation, it would seem that the chipset only supports PCIe 1.0/1.1, but all documentation on the MacPro3,1 that I've seen suggests that the first two slots support PCIe 2.0 (which I presume is direct into the CPU rather than the northbridge).

Any confirmation on the spec here? As well, why would GPU-Z only be reporting PCIe 1.1? Could it have something to do with the fact that I have a USB 3.0 card in slot 4?
If that is a PC (non-EFI) graphics card, running it in Windows on a Mac (Bootcamp) will reduce the speed to PCIE 1.1

You must have an EFI flashed card to run at PCIE 2.0 in Windows on Mac machines. Drivers solve this issue for some PC (non-EFI) cards in OS X, but not Windows.

Real world gaming difference between 2.0 and 1.1 will likely be negligible, and your bottleneck will most likely end up at the CPU or OS X drivers. Generally I see better performance in Windows.

For reference I run a GTX 1060 (non-EFI) on a 2009 Mac Pro; my benchmarks and real world gaming are all better in Windows, at the PCIE 1.1 speeds.