My first guess would be you have a bad riser.
Are you using an x1 to x16 riser, or an x16 to x16 riser? Either should work, but there happen to be some x16 to x16 ribbon-style riser that are made by more reputable manufacturers.
I will look into hive OS thx. I'm using x1 to x16. Riser looks made very well nice soldering and so. For some reason my PC doesn't recognize it if I put in to x1 which is light grey color, but it's there if I put it in blue bottom one. If it is riser fault I tend to believe only GPU which is connected through riser would have bad performance, not the. It is which are connected to x16 directly. Really strange. To clarify my MB is Asus p9x79 pro.
Don't trust risers... i have a box with >100 of them, all bad, over time, i have a constant stream of risers failing. Just imagine them like disposable pieces, because that's what they are..