We added a new blog post about how to fix the assets created for Unity 4.x, especially the trees with transparency. Read the full article here Saradonhildiadventures.com
Trees must use the Nature/Soft Occlusion Leaves and Nature/Soft Occlusion Bark shader. In order to use those shaders you also have to place the tree in a special folder that contains the name "Ambient-Occlusion".
So, to fix this: