Try allowing the display of hidden files. There is some malware out there that hides most of the files that you seem to find missing.
Go to Control Panel -> Folder Options -> View (Tab)
Check the box “Show Hidden Files and Folders”
Remove the check from “Hide Protected Operating System Files” (Click yes to confirm)
“OK” your way out.
The files may then show up “ghosted”, indicating that they are hidden. Right-click on the files, select Properties, and un-check the “Hidden” box to make them generally visible again.