Render view & Batch Render different results. Need help!

I have a huge problem with batch render and render command outside maya not generating the result i expect. I have a fairly complex scene with several layers, and some parts on those layers use material overrides.

Preview Rendering a single frame looks like I want but when i render using batch or outside maya workspace the result is different. It seems like something happens and maya completely ignores or has a free will to assign shaders & material overrides on parts where i don't want it to.

Placement and UV mapping also seems a bit messed up for some textures. Anyone have any idea what could be wrong? I can't seem to find anything wrong with render settings and layer settings.

Below is an example of the reults, from one of the layers.

Have you tried rebuilding your render layers? Remember that it's almost always a bad idea to do texture work (other than layer overrides) while you are in a render layer other than the masterLayer. Also remember it's a bad idea to have mulitple textures on different faces of a single poly object. These things almost always break render layers in some way.

Do your modeling and UV work in the master layer. Separate polygon objects so that each object gets only one shading group on each render layer. Does that help?

Worst case scenario, you can try using one of the scripts that lets you render a sequence from the Render View, if that is working correctly for you. 

-robin