That's probably the only slot I didn't test earlier, but after your post I did. Works fine in bios, but in Windows it's still giving error 10. Not matter which slot, which PCIe generation I set it to, and no matter what I disable of onboard devices. Currently only SATA and two PCIe slots are active in the mobo bios. One for graphics and one for the raid controller. I even tried different graphic cards and hard drives to rule out some freakish compatibility issue. No luck.
Everything else I throw at it, like other raid controllers, more graphic cards, FireWire cards etc, works fine in any port under any load. And the raid controller works fine in any other computer I've tried except the one I need to use. So I guess it comes down to this; the P9X79 mobo is incompatible with RS3WC080. At least that seems to be the case with my specific samples of the two.