2 PCI-E 6-pin connecters malarky

Hi everyone, I've just upgraded my old desktop with a new 500w PSU and ATI 4870. After playing a few games it felt like the GPU wasn't performing as it should be. So I thought I'd benchmark my computer with 3D mark 06 and compare the results with this lovely website. I did that and my graphics card's point are of a 8800 on SM2 and even worse on SM3. I know my CPU isn't the best (Intel core 2 1.86x2) but 3D mark says my computer is at the bottom of the chart when compared with similar computers, but here's the thing which has been bugging me.

My graphics card came with a little book saying the only good connection for my graphics card is 2 PCI-E 6 pin connectors, and a 2 4 pin converter to 6 pin is a bad connection. I asked a couple of mates and they said it shouldn't matter. I'm going to get a new motherboard and cpu soon but do you guys thing my GPU's performance has been hindered the fact is is only connected directly via 1 6 pin PCI-E connector and not 2?