Render Bug When DupliGroup an Empty via Script

Hi All,

I am working on a script that takes an image as an input. The script extracts the alpha channel from the image and uses that for the Z-Scale of each object.

Objects are layed out in a grid like fashion using Empties. The empties dupligroup a single cube object.

This all works fine and it looks correct in the viewport, but when I go to render the scene, the cubes are missing faces.

I have posted images and a BLEND file here:
http://blenderartists.org/forum/showthread.php?p=1261702#post1261702

I am kind of stuck at this point. I’m sure it is something to do with linking into the scene, but I can’t figure it out.:spin:

Any help is appreciated.