I had the same problem with a robot animation.

The head of the robot was duplicated in batch render where all looks fine in view port and render view.
MichaelC, your workaround might not be a permanent solution of the problem, but it worked for me in this case. Thanks

I'm using Maya 2012, but this doesn't look to be related to a specific maya version. If anyone could explain what goes wrong that would be great.