Have a look here: T39828

Animation of render layer is not supported (anymore).

@Willi (willi) - actually that's a different property, I'm trying to animate the actual render layer toggle on and off - which worked in 2.69.

I think the problem here is that render layers are copied into the renderer state data at the start of the render job:
https://developer.blender.org/diffusion/B/browse/master/source/blender/render/intern/source/pipeline.c$516

This means that, even though the anim data is correctly evaluated and updates the render layer flags in the scene render data, this has no effect on the currently running render job's layer flags.

In general this means that any animation on render layer data is effectively not supported. I can think of 2 possible "solutions":

1. Rebuild the render layers list of the render job for each new frame
2. Accept that render layer flags (and possibly other settings) cannot be animated and enforce that in the API (not so nice of course, but may be cleaner design)

Thanks to all, its a great feature to have!