Witcher 2 doesn't work with 7970 Crossfire right now at all... and I'm not sure they have any intention of fixing it, so it's possible that it's just broken for 6950 crossfire as well.
Anyawys, what resolution are you playing at? You're probably losing some performance for having x16/x4, but that does seem odd.
Do you have MSI Afterburner installed so that you can monitor GPU usage during your tests/benchmarking? That will show you if both your cards are being utilized or not.
I'm playing at 1080p, and I just ran Afterburner with the FC2 benchmark. Gpu2 got 100% use, GPU1 got 50%!!! WTF!?