An analysis of the tech specs of the 30 LGA1156 motherboards from ASRock, ASUSTeK, Gigabyte, MSI and Intel with a second x16 PCI-Express port shows up an aspect of the spec that may go unnoticed at first but which is nevertheless important.
On 12 of these motherboards the second x16 PCI-Express is not connected from the LGA1156’s processor to the PCI-Express controller with 8 lanes (the 1st PCI-E port is 8 lanes) but with 4 to the P55 Express.
What’s more the lanes linked to the LGA1156 processor function at 5 GT/s and those linked to the P55 at 2.5 GT/s: this means one x16 PCI-Express port at x4 with the P55 functions at 1 GB/s in each direction as against 4 GB/s when at x8 with the processor!
This reduced bandwidth will of course have an impact on performance, making the use of this port for a high-end graphics card problematic. Of course this is an economical choice for motherboard manufacturers as it simplifies the design of motherboards, but it is easy at first not to notice this nevertheless important aspect of the spec. It would be simpler for users and more honest on the part of manufacturers if the ports reflected the number of lanes physically as is the case on the Intel DP55KG motherboard for example.
Moreover you will note that there is a motherboard with a x16 link for the second port, the ASUSTeK P7P55 WS Supercompter that uses an additional nForce 200 chip.