You baked the Color(Diffuse) but you also need the Transparency(Alpha)? Select the Alpha map option but rename output file to the same name as the Diffuse map. Doing so puts the alpha into its own channel in the diffuse.
As Kratos mentioned, just render your diffuse using an orthographic camera. You can also get normal out of this by setting up a certain kind of light rig, but it can be a pain to set up. In all honesty for generating grass cards you might as well make the grass blades high poly and avoid the headaches with the alpha planes.
I cant bake the color(diffuse); because the polys with a transparent leaf texture applied, occlude/overlap each-other. It is the same situation as _kratos's. However, unlike kratos, i cannot use his solution because i am not rendering a flat texture, but baking a highpoly mesh to lowpoly mesh. I need to be able to bake…