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Marmoset & alpha maps

I want to first say I did a search on this issue and found one thread.
http://boards.polycount.net/showthread.php?t=61548&highlight=marmoset+alpha

It was mentioned that I need to have seperate meshes to get alphas to display properly, or am I misunderstand? When I tried this, I got the same result. Let me show you the issue.

I am currently in the process of texturing a car, and since Maya has trouble with alpha's, I wanted to use marmoset toolbag to help me instead.

Marmoset is not displaying my alpha properly on only a certain part of the mesh.

marmoset.jpg

I want the windows to be semi transparent. I have .tga diffuse map with an alpha channel, which is currently set to be fully transparent on the windows. As you can see, the windows are indeed transparent, but only to the background. I need to be able to see inside the car. Why is it doing this?

To add to the confusion. I tried painting alpha on other parts of the uv. When I do this the alpha actually displays perfectly (apart from the windows). I can see through where ever I painted, just as you would expect. I do not understand why only the windows will not render properly.

The windows are single poly planes, which the normals facing outwards. To note, I have also tried having boxes for the windows and I get the same effect. I have checked over the mesh numerous times and can not find anything wrong with it. (apart from my bad modelling skills :P )

I have tried playing with the alpha threshhold (I do not understand what it does however) and after a certain value, the windows do go transparent. I tried this with 50% gray and tweaking the threshhold still makes the windows just disappear.

I have tried the other blending modes but they are giving completely different results to what I want.

I hope someone can help me, thanks all.
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