Rendering multiple layers works fine for me in 2011, but it used to only render the layers one per session in 2009. So it could be a version issue you were having.

We've had similar problems on our short film. One thing to look out for is that if you have some referenced and instanced objects you may need to import the references into your scene for Batch...

We've been using a geometry solution to making our Heavenly clouds for our short film but we're having some flickering problems and Id love to solve the issue or find a good replacement....

Here's a few images from some of the completed shots on our short film.
http://dl.dropbox.com/u/1289261/DevilsAngelsDating_Animation_Panic_Devil.jpg...