Get a copy of GPU-Z and run that. PCIe allows the graphics card to clock down to a lower bus speed to save power when the highest speed is not needed. However, GPU-Z (as opposed to CPU-Z) has a graphics test that it runs in a window to force the PCIe bus speed to run at max speed.
i.e. my system has a Radeon HD 7970 installed but when it is running on the windows desktop it only runs at PCIe x16 @ 1.0. However, when I run the GPU-Z graphics test, it steps up to PCIe X16 @ 2.0. (I don't have a PCIe 3.0 motherboard)
I'm alredy running GPU-Z ??
And it's showing @x16 1.1 when idle. It steps up to x16 v2.0 when running the render test.