Some of the trees leaves have issues with transparency, why is this?
The material settings:
Image (by Krzysztof P. Jasiutowicz, source :

Some of the trees leaves have issues with transparency, why is this?
The material settings:
Image (by Krzysztof P. Jasiutowicz, source :

For this particular problem it seams like your shader, and image's alpha are not the problem, but rather z-fighting. When there are doubled up faces with transparency the z-fighting will not have the characteristic black look, but rather strange transparency artifacts (much like your render).
To fix the doubled faces, check your particle settings to see if there any duplicated leaves. If there are more particles then places to emit them, then they will get doubled up.
Here is a cube with 8 vertices, the particle system number for both is set to 32. The only difference in the two is for cube on the right I gave the particles some randomness.

It seems like the problem is that the Alpha channel of your image is not 1; This leads to some translucency sneaking through where it shouldn't. To fix this, you can use many methods, but, probably the best is to use a Brightness/Contrast node:

If you put that node between your image's alpha and the Mix node, and set the contrast to a rather big value, such as five, the problem should be fixed.