The HF engineer in me cries "OMG THAT CABLE LENGTH!". Do you have somewhat shorter USB 3 spec cables to try this with? Maybe some of the nVidia cards are having trouble with signals getting distorted on these long cables.
Christian
Those risers aren't actually using the USB protocol - they're really just simple extension cables with USB ends on them.
the RF engineer in me knows that. The cable length introduces delays, attenuation and nonlinearities that may be well out of spec for the PCIe bus.
I guess that's why you're the designer of this program. I guess i'll stay in school and keep studying computer engineering, maybe i can help you out at some point.