I had the exact same problem. It took two times of bringing in my xfire for the techs to finally figure out that it was indeed a faulty secondary pump. I haven't had poor acceleration since. The reason for the bad acceleration is because you're basically losing boost. When the water pump malfunctions, their is no flow to the intercooler which means the water in there is stagnant. This sitting water then heats up, which also heats up the intake charge going to the supercharger. Because the supercharger has a sensor to monitor intake temp, it will automatically disengage the supercharger via the pulley when the intake temp gets too high. This then means no boost. After my car was fixed, they told me that my intake temp went down almost 100 degrees!! Since then I've had even better acceleration (not a huge difference) and better mpg.

-Josh