Most AV scans have an option for doing a root-kit scan but you have to select it. I use Kaspersky but I believe the MS Security Essentials has one too.
It may take a while to run it since it has to dig deep and the root-kit actively hides itself.
If the root-kit is deeply embedded, you may have to reload the OS from a safe source (like a CD). You can try a system restore first and have it restore from a previously recorded "restore point" prior to the issue.