Change in configuration on MSI motherboard

I'm trying to change my PCI 2.0 x16 to run at x16 instead of x4

If HDMI is in PCI-E port 2 "Geforce GTX 960" it run at x16 while PCI-E port 4 "Geforce GTX 960" run at x4
If HDMI is in PCI-E port 4 "Geforce GTX 960" it run at x16 while PCI-E port 2 "Geforce GTX 960" run at x4
I want both port 2 and 4 to run my GPU's at x16 , i have try'd contacting MSI "which is my motherboard" for support but did not help and i have try'd using the PCI-E 3.0 patch but that did not work either. best workstation motherboard

Both GPU's are able to run at x16, how do i force the odd one or both to always run at x16.
Mother board : MSI AMD 990FXA Gaming
GPU : Geforce GTX 960 VRAM 4G x2
Power Supply : 750 watt
Ram : 32G
Processor : AMD FX(tm)-6350 Six-Core
Win 7 Ultimate



ORIGINAL TITLE : PCI-E x16