a 5 minute animation is taking me so far 3 days to figure out!!! I did a simple text extrude, animated a camera, but a white shader on the top text, a pink shader on the bottom + a black plane with reflection... (it took as long to do than to write it)... when I did a "render current frame", it showed up exactly as I wanted... then up I went with batch render to do it all, strangely, the sides are properly lit, but the faces came out black, like the light didn't hit them... I tried brining up the ambiant color, nothing does it... any clues..
If you are using the hardware renderer you are subject to graphics card glitches. If you are using Mental Ray for your preview render within the GUI, you have to make sure your batch render is also using Mental Ray to achieve the same results. Add the '-r mr' flag to your render command--otherwise the Maya Software Renderer is used by default.
I'm honestly not sure if that's the cause of your problem, but it's all I can think of.