I am having a similar issue. I do a local render and the image comes out looking great but when I batch render the image is much flatter, some of the textures don't seem to work at all.
I am using final gather and it seems that its not using the effect in the batch render. I also loose glows and incandescence but fur looks like its on fire.
I don't have any render layers and Im not sure how to set up a final gather render pass. Would NextDesign's code work to render what I need? And if so how do you use that code in Maya 2010?
I have attached a RAR with a local screen capture jpeg of an .iff and a batch Tiff Frame so you can see the difference.