If you eliminate everything else and want to probe the rootkit thing, one place to start could be Microsoft RootkitRevealer.
It's a "TechNet" article so it doesn't have a doc number for easy reference, and it probably assumes a skill level that you have; but some others (more likely to need it?) may not be able to get much from trying to use it.
Disk cleanup and Disk "Check for Errors"1 could show something simple, so I'd do all the normal stuff before worrying about exotic infections (Right click your drive in Windows Explorer, Properties, Tools).
1 Check for errors can take a long time, and if you check the "try to recover sectors" box can take a very long time, so plan accordingly.