Knowing exactly what is happening when you create new scenes within your model is very important to know. What you do with your object within your scenes and what affect it has on any other scenes you have created is another one of those pieces of information you need to find for yourself when using Blender. What information is carried over to the new scene as it is created with the different options (layer location, objects xyz position, material etc.)? I will be doing some experimenting tomorrow morning, organize this information and report back then.

See ya then.