Probably not an issue in your case, but another reason may be that Windows won't show you the space taken up by files you don't have permission to see. (or at least directories, perhaps it will for files). It'll still report it under the disk usage if you look at a disks properties, it just won't show it to you if you look at a directories properties.

At least du (the unix equivalent) warns you when it can't descend into a directory to see how big it is.

Matthew