Baking textures with decals

Hello guys, I need some help with this:

I am baking diffuse texture from hi-poly mesh to the low-poly mesh in Blender Render.

Hi-poly mesh has several materials, each with diffuse, normal and specular map. It looked a bit plain, so I decieded to add some decals on it. I can’t project them from empty, because my texture contains 16 decals and I am using only one of them (also it was still repeated over the whole mesh in viewport, even when it was set to clip), so I added several planes and unwrapped them to fit the decal on the texture. Then I needed to get rid of the edges - background between decal pictures on the texture, so I enabled Z transparency defined by the alpha channel of decals texture and it all looked fine. This is how it looks in viewport:

But when I bake the diffuse texture to the low poly mesh, edges of the decal will show up again. This is a picture of baked texture:

Is there a way of baking textures how they actually look in viewport, or is it just some alpha value somewhere that I should change - does anyone have a solution for this?

Maybe try doing it in Photoshop/GIMP

I have the same problem! any solutions?