MSI has released a batch of slides that explains what native PCIe Gen. 3 actually is and also bashed the competition (Gigabyte to be precise) and their "Gen3 ready" claims.
According to the full set of slides from MSI, Gigabyte's full lineup of marketed Gen3 ready motherboards contains a single motherboard, Gigabyte G1.Sniper 2 that actually has the real native PCI-Express 3.0 support. As MSI explained it, in order to have native PCI-Express Gen3 you have to use actual Gen3 switch chips, capacitors and resistors in order for things to work as they should.
Unfortunately, Gigabyte's lineup doesn't include those and when tested, Gigabyte's P67A-UD4-B3 actually switches to Gen1 x8 instead to Gen3 x16 like it is the case with MSI's motherboard. Of course, we can't be sure as we are yet to hear the Gigabyte's side of the story and hopefully we'll hear it pretty soon.
You can check out the entire document here, and we are pretty sure that Gigabyte's answer will follow pretty soon.