I've had success using the Bit-defender rescue CD in the past to remove infections from a machine, It's a linux based live CD with the Bit-defender AV built in which means you're booting from a clean environment which should in theory help where a rootkit is suspected. (As you are booted from the CD instead of into the compromised OS on your hard-drive)
If it detects a usable network connection it will download the latest definitions before starting to scan the system.
http://download.bitdefender.com/resc...-rescue-cd.iso