How are the fans in your case set up? If you've got more exhaust than inlet fans, then the fan in the GFX card works at a much lower efficiency, because air ends up being sucked against it's flow.
I tested this on my case by the scientific method of taping a strip of paper above the GFX card outlet, then turning the fans up and down. There's a huge difference in what comes out of the card's slot depending on how high the other fans are set. With the inlet fans up full and exhaust on low air comes blasting out of the slot and the paper is horizontal, with the exhaust fans on full and inlets on low it barely moves.