restating somewhat what lord said above;
the reasons for the tiny dens are because when you changed up the sizes and re-saved the objects, you must not have created custom groups. to fix this you will need to re-group your objects and more than likely replace them on the map itself.
when editing, or adding new objects via object maker to the game, you ALWAYS have to make custom group files. do not save the files into any of the object groups that come with the game.