There is also the issue of file links :/
They have been around a long time but until vista Windows itself didn't use them much, now it does. The \Windows folder is full of them and depending on wher eyou are looking for a total file size or what program you are using to so it yo ucan get some pretty bogus numbers because it counts the size of the original file, then every single file link to the same file.
If I can remember when I get home I can post an example. You can right click the \Windows folder and get a value for the entire folder size. Then, inside the windows folder is another folder of hard links to nearly every system file and that folder alone looks like it is the size of the entire Windows folder even though there is really "nothing" in it (nothing taking up space that isn;t already counted externally anyway).
Is it possible that a daily restore point is making a snapshot of the critical system files as hard links, therefore making it appear that the windows folder is growing when it really isn't?