Problems Baking Alpha Map

I made a leaf texture with an alpha map with the aim of rearranging several of them into a branch and baking those onto another texture. I managed to get the leaves to render as transparent but when I was baking them, the alpha map was ignored and the see-through parts of the texture appeared black and occluded other leaves. Does anybody know how to fix this?

EDIT:
A small image to illsutrate the problem. Ideally I would want to see the silhouette of the leaves against a black background.
http://img407.imageshack.us/img407/3410/leafproblem.png