Layer0 is still there?

[djh]

How come Layer0 always appears? If when I deselect it and update Scene 2, go to Scene 1, and return to Scene 2 ... Layer0 is still there?

[Box]

If you are using layers correctly Layer0 should remain as the active layer and shouldn't effect your scenes.
If you are using layers incorrectly anything is possible.
Attach your model so we can see what you have.