I've encountered a problem with a transparent material I created to resemble a form of glass. In the scene I have set up, I have a multitude of X "Dummy" Trees propped up in the background to fill the skyline. However, as you can see through the image, the trees that are not behind the POV with the glass look fine while the ones that are behind it act like their alphas are not being used.
Each tree is an 'X' plane with the image of a cycled rendered tree plastered on it. It is made so that only the tree is visible, and the rest of the picture is transparent.
Is this a problem with the texture made for the trees or the window? Since I also noticed that this same kind of glass created some weird effects on UV textures in another part of this scene.
It still seems to be prevalent in the trees, albeit some trees, (which I have pointed to), have the problem fixed, while others in the background still have the black rectangles. To the right is my selections for options and shadow.
Here is a copy of the blend file with the stuff needing fixing selected.
Here is the tree files for the Dummy's: http://imgur.com/a/HTOhC