Using v2.73, cycles and a very simple scene: an array of cubes, no big deal.
![enter image description here][1]

If I set the shader's material to transparent, the cubes in the foreground do become transparent but those far away in the back do not disappear completely and this strange dark *things* appear (visible in rendered mode and in final renders)

![enter image description here][2]

I've played with the clipping distance on the viewport and camera, but I can't figure out how to make those *ghosts* go away...

Blend file **[here][3]**

Any thoughts?


  [1]: https://i.sstatic.net/7vHzU.png
  [2]: https://i.sstatic.net/9BC5t.png
  [3]: http://www.pasteall.org/blend/35243