Are you placing your trees on the second and/or third layers? If you place them on the first layer, in editing view you'll notice there's a white border around them that oughta be transparent, that's because there's nothing below it, except for the black, which is what you'll see in game.
So you place your grass and stuff on the first layer, but the trees/plants/objects go on layer two and three, basically. If that' s not the problem, please explain further.
Also this had nothing to do with this topic, but aight.