The problem with rootkit detection is that genuine system files will also be detected and you really need to understand what you are dealing with.

More info about rootkits:

http://www.5starsupport.com/tutorial/rootkits.htm

http://www.guard-privacy-and-online-security.com/how_to_defeat_a_rootkit.html

http://searchwindowssecurity.techtarget.com/originalContent/0,289142,sid45_gci1086474,00.html

If you suspect you might have a malicious one, best to get expert support. You can rely on the help here: http://www.virusvault.co.uk

If you don't already have it, download and install Windows Defender and also the latest Malicious Software Removal Tool from Microsoft. Both of these will provide some degree of protection against rootkits.

Another useful tool and support forum is SysInternals' RootKitRevealer and you can submit the report to their forum for analysis

Forum: http://forum.sysinternals.com/forum_topics.asp?FID=15

Read up about Rootkit Revealer and download from here:
http://www.microsoft.com/technet/sysinternals/utilities/rootkitrevealer.mspx

Read about how to use the forum here:
http://forum.sysinternals.com/forum_posts.asp?TID=2351