The problem in the chipset was traced back to a transistor in the 3Gbps PLL clocking tree. 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.