In Unix-land, this is almost invariably caused by one of two things. The first is that you mounted a filesystem at a mountpoint that already contained data, and the new filesystem is hiding it. While it's possible to mount a filesystem as a subdirectory under Windows, virtually no one does it, so this is terribly unlikely. The other, more common, issue, under Unix, is that a program has a handle on a file and then the file gets deleted from the filesystem while the program still has its filehandle open. In effect, this removes the file from being listed in any directory, but it doesn't free the disk space until the program closes the filehandle (or exits). I don't know if Windows works similarly, but it might be worth checking into. You could reboot the system to make sure. (Somehow I doubt this is it, since Windows gives you access errors when you try to open the same file twice, but what do I know?)

You might also want to try some sort of disk usage utility. It might point you in the right direction. I use Scanner.