@JCPalmer : I see that you have posted a new version of the BE - version 5.
Does it have a minimum Blender version Jeff ?
cheers, gryff
A quick example of lights and "This Layer Only" - see image below.
Two objects, cube and sphere in two different layers. The layer with the cube has a Hemi light( white) that illuminates all layers. The layer with the sphere has a point light (red) with the "This Layer Only" box checked.
Result - cube lit only by the Hemi, sphere by both lights.
cheers, gryff