if you dont have access to view folders contence the it will course this
corupted downloads can aswell eg DVD download as a curupted zip/video file that file system cant read but still has a size on the disk
hidden files as well if you are useing the select all on the drive way to get total size make shore that hiden files and folders are shown (might be wrong about that but best to beshore).
can you remember when you lost the space?
give ccleaner a go http://www.piriform.com/ccleaner