The rootkit was found by Malwarebytes, but it was strange indeed. This root kit was attempting to reach a malicious site, which Malwarebytes Pro was blocking every 15 minutes, which I could see from the Mbam log. After not finding the rootkit for several hours, it suddenly, after another 15 minute, found the rootkit, which it removed. Since that time the IP block has not occurred.
I opened a case on Mbam, and they did a very thorough job of helping, including scanning logs of my system, and suggesting various pieces of software to monitor my system, and helping me to use Combofix.
I can only say the buying Mbam Pro was really worth it.
The help at Mbam also suggested amending the host file. Take a look at: http://www.funkytoad.com/content/view/13/31/