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Not sure what you exactly mean. alpha layer is pretty straightforward as you probably know. black is transparent, white not, grey values somewhere between (there's lots of guides to can google about it).
In some rare cases I have noticed if you have a couple of targa files overlapping each others the part where they cross might not show the transparency at all. This applies to skinning however, no idea if it's same with your own LUA windows.
Perhaps up a few screenshots of your problem for us to see and that might help with locating the problem.
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