I think the trouble is SB-E had a 'draft' PCI-E 3.0 support before the spec was officially finalised and something changed, something to do with latency/timings and it's not 100% supported anymore. When the platform first came out it was advertised as "8GT/s PCI-E" and not 3.0 but Intel don't even advertise it as that now, they only say that it supports 2.0.
The first real wind we got of it was when NVidia very responsibly acted by limiting their cards to PCI-E 2.0 because any stability issues would likely be seen as a GPU problem, NVidia got a bit of flak for basically being proactive in protecting their customers from possible issues.
Running in 8GT/s mode is at the users own risk and looking back I'm wondering if this is the reason I had such a torrid time with the 7970 as this is the platform I was using it with.