It could indeed be the saves! The game checks for a "DLC enabled" variable to play the DLC scenes, so your saves from the free version would have this variable set to false and would fail to trigger the scenes... Sorry about that!
Have you tried starting a new game in the DLC version and choosing "Start from another chapter" to start from chapter 3? That should let you see the DLC scenes without having to replay chapters 1 and 2!