what's happening is that you're probably ripping 9gb dual layer dvd's and then copying them over to 4.7 dvds.
but clone dvd doesn't shrink the movie to fit on one disc, it does however split it into two dvds.
so when youre done recording on just one disc you end up getting about half of the movie.
i also learned that the hard way. if you're looking for simplicity use DVDXCopy. it will shrink it for you and fit the entire dual layer disc on one dvd.