MSI put together a presentation to detail information on what it feels is a true PCIe Gen3 motherboard. MSI is pointing out that, from its view, Gigabyte's claim on having 40 PCIe Gen3 boards isn't true.
MSI shows that its motherboards utilize Pericom 34xx (Gen3) switch chips, whereas Gigabyte utilizes Pericom 24xx (Gen2) switch chips. To fully utilize PCIe Gen3, all components are required to be Gen3 compliant to operate at 32 GB/s (CPU, PCIe Slot and GPU).
MSI said that it did some PCI-Express electrical testing using a 22 nm Ivy Bridge processor sample to show the bandwidth seen on Gigabyte's P67A-UD4-B3 and MSI's MSI Z68A-GD65 (G3).
MSI states through their review that the only true PCIe Gen3 ready Gigabyte motherboard is the G1.Sniper 2.
See more on this topic from MSI's Media Page