This is quite the issue I've been having here. To sum up, I've got subD geometry in my scene, I'm rendering an animation, and I'm doing it through mental ray. None of the issues I'm about to describe occur within the Maya Software Renderer. I'm running WinXP SP2, Maya 7 with mental ray 3.4.5.2.
Whenever I batch render a scene using mental ray, one of my pieces of geometry (the character's body) disappears. Gone. The Primary Visibility and Visibility attributes are set to "on", and any reference to hiding the geometry in the mental ray field is turned "off". The only thing I can think that I did which was.. I don't know.. strange, was boolean-unioning a few pieces of geometry together when modelling my character. But I've since deleted the history multiple times over, and created entire UV maps with custom files for color. I can't imagine how it would be connected.
Here is a screenshot of a single frame (non-batch):

And here is that exact same frame rendered as a batch:

It is using mapped UVs to describe the color node. It has a poly-cage which is hidden. This is a screencap of my mental ray performance/memory/etc options:

I'm really not sure what else to do. I'm thinking of just writing a MEL script to pretend to batch render.. but in reality just loop through a specified number of frames one at a time.