I like the new plug in 3 first of all. takes a little getting used to, since I am used to the other one, but much more powerful.. Great work on it.
My scene was setup in mental ray. I set a forest to some parameters with 4 or 5 types of trees. In the material editor, I wanted to simply drag and drop some new trees on the ones I defined from the modify panel. (hope you can follow my procedure) in the diffuse and opacity maps. When I did this on next render, no trees. I could do this with the old plugin.
FYI. Setting the blur, in coordinates pullout (as opposed to the defuse) on the transparency maps will cause a crisper tree.