Compressing the files should give you an RGSSAD file that contains all the maps, images, whatever else is in the game. If you just burn the project to a CD and give it to someone, they can open it up in RPG Maker and mod whatever they want. Compressing overcomes this.
As to what's causing your problem - I've no idea. If it were happening to me, my first step would be to reinstall RPG Maker and try it again, to see if anything messed up along the way.