I have exactly the same concerns. I am backing up a 9G partition on a test server, no databases, but CPS is only showing about 3G. I can't see any files in particular missing but it gives me a very uneasy feeling.
There are no databases, and anyway shouldn't I see some sort of reporting if something isn't getting backed up? Restoring all the data doesn't seem like a particularly great way to prove this.
Andy