Troubleshoot render layers do not render correctly when exporting a .mi file
 
 
 

When exporting your scene as a .mi file, if your scene consists of more than one render layer, you must select the Output file per layer option in order to obtain renders in which your render layers do not affect each other.

This restriction applies because mental ray interprets each single .mi file as a sequence of "incremental changes" in the scene. Therefore, completely independent render layers containing different sets of objects cannot be represented efficiently in a single .mi file.