It's the images you're using. I had a hell of a time with this myself. It seems alpha plane interpretation is pretty iffy with TG2. There is a new set of leaf textures available at the guy's web site. The textures included are jpeg, with the alpha plane split into a separate image. These work fine and avoid the whole alpha plane issue.
There is another issue with the generator that no-one here seems to have picked up on. The author seems to have trouble with his model orientation/vertex winding. With the original version of the program, models were incorrectly lit and I would have to click the 'flip normal' switch to get the seed to appear on the outside of models. The new version (1.3) of the program has corrected this - the same models now appear correctly lit and the seed appears on the outside, without having to click 'Flip Normals'. The models are still mirror-imaged, though - put ivy on the left side of a model in the generator, and any other program (PoseRay, TG2, MilkShape) will show it on the right side of the model.
This may also affect the orientation of the leaves, but I'm not certain of this. The author notes on his site that most of the images submitted to him have had the leaves pointing in the wrong direction. If you look at the original leaf textures, the leaves point to the left. All the images in the new texture set point to the right. Sure enough, if you use the original textures, the leaf tips point back along their stem, instead of in the direction the ivy is growing. I suspect that the author's model orientation problem tricked him into creating the first set of textures incorrectly, but I'm not sure he understands the real problem - after all, the generator is still rendering models backwards.
So use the new jpeg textures that contain a separate image for the alpha data and it should work.
