I have a 'problem' with SLI 480GTX on a X58 motherboard - P6X58D Premium.
GPU-Z shows one of the 2 working in 'full' PCIE 2.0 X16, but the other stays in PCIE 2.0 X8.
HWINFO32 shows v2.0 X8 for both, in 'idle mode' 2.5Gb/s and during (windowed) Furmark still X8 but at 5.0Gb/s.

Would be interesting to know if they really are running in v2.0 X16...

And yes, I have the MB BIOS set to 'x16-x16-x1' for the 3 PCIE x16 slots.