I think not that that is the problem, drow...
The problem is that you have different shades in your alpha channel. That means, there isn't only black and white, but also different shades of grey. Behind these half-tranparent parts of the texture other textures with alpha channel will hide.
If you look at BIS' orignal textures for plants, you will notice that they also only used plain black and white in their alpha channels. Try to reduce your alpha on these two colours, then your problem should be solved
