Using v2.73, cycles and a very simple scene: an array of cubes, no big deal.

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)

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...