A CD also contains a "catalog" of all the files on it, which takes up space (not sure how much). Obviosuly the more files on the CD the larger the catalog will be.
Also, individual files dont always fill the space they are allotted on a hard disk or CD. All devices like hard disks or CDs crate invisible "grids" to hold files in (a bit like graph paper), and if each grid is not filled up it can leave lots of empty "spaces" all over the hard disk or CD.
Maybe all these "empty" spaces is where all your missing space has gone.