What do you mean by 3 layers? That you organized your scene in layers in the world browser? If so, check your render settings, it may be that you have the "render active layer only" box checked.

Don't mind the colour of the camera in that panel, this colour is only for display, plants have a green colour, lights a yellow colour, but it's just a way of visualizing your scene elements faster.

Could you prvide a screengrab of the Vue interface of your scene? What atmosphere are you using?

A suggestion: always make a small render of the scene before the final one, to avoid surprises.

Another thing: check the atmosphere editor, and see if the light balance isn't all the way towards sunlight. If so, push it to the left at about 50%