Maya :: How To Use Xgen In Pipeline

This is my first time trying to use Xgen in our pipeline so I am hoping this is just user error. I have a Xgen discription that populates a plane with rocks. I have gone through all of the suggested set-up steps in the user manual for batch rendering.
 
When the files render out all or some of my rocks will dissapear for 1 frame and then come back spuratically There doesn't seem to be a ryhm or reason to which packets or which machine it happens on. I have re-rendered the scene twice now and each time the anomolies occur on different frames. 
 
Rendering using mental ray at 32 bit with render passes