Additional details have emerged on Intel's 6-series chipset flaw. AnandTech has learned that the problem was traced back to a single transistor in the PLL clocking tree for the 3Gbps SATA controller. Anand explains:
The aforementioned transistor has a very thin gate oxide, which allows you to turn it on with a very low voltage. Unfortunately in this case Intel biased the transistor with too high of a voltage, resulting in higher than expected leakage current. Depending on the physical characteristics of the transistor the leakage current here can increase over time which can ultimately result in this failure on the 3Gbps ports. The fact that the 3Gbps and 6Gbps circuits have their own independent clocking trees is what ensures that this problem is limited to only ports 2 - 5 off the controller.
The kicker is that this transistor isn't even needed for the chipset to function correctly. At least that makes the solution a simple one. The new 6-series chipset stepping will have the transistor in question disabled.
Interestingly, it appears that the problematic transistor was inserted into a later B-stepping of the chipset that eventually shipped to customers. It wasn't present in earlier steppings, which may be why the flaw wasn't detected earlier. The problem was only discovered when the chipset was run at higher-than-normal temperatures and voltages to simulate long-term usage.
We're still waiting for mobo makers to communicate their plans for repairing or replacing affected boards. MSI has joined Gigabyte in halting shipments of affected motherboards and asking that products be taken off store shelves. Asus has yet to issue a formal statement on the matter.