Operator error. Autodesk changed the way renderlayers used to work in Maya 7 (I think it was 7). I used to use the right button menu in the renderlayers panel to assign shader overrides. Seems it doesn't work that way any more. When you do that, it creates an override for the entire layer. Hence all of my objects looking the same. Now the workflow is to select your render layer and just assign the shader as normal.

I'll never understand why software companies deem it necessary to change things that aren't broken. Maybe it justifies their maintenance fees.