Extending PCI

Hello,

I have created a PCI extension adapter that extends a PCI port by 6 inches. I'm using this to place a Comtrol Rocket PCI card in a 1U case. The Rocketport driver in the kernel can see the card and detect the number of ports on an external expansion box but I'm not getting data in and out the ports. All this works fine without the extension. My question is there a way in the driver or another part of the linux kernel to change timings that will solve this problem?

Thanks,
Chris