I have Blender 2.7, and as a backup 2.69. I have three render layers, each with only one or two low-poly objects. I’m rendering in Blender Internal (yes, I have my reasons). Hooked all three render layers together with Alpha Over nodes at “fac” 0.5 and then the whole shebang goes to to the composite node. The setup is simple and classic, and the viewer node displays all three layers in perfect order and harmony.
Then I render it as a still image and only the 2nd render layer renders. All three render layers have exactly the same settings, including “combined.” All three scene layers are checked, and the camera and light are checked into all three scene layers. If I move around which object is in which render layer, Blender still renders only the object(s) in the 2nd render layer. Same if I move them around in the scene layers.
It’s times like this that I wish I had hair on my head to tear out LOL.