I know my skin was designed correctly because a website viewed it correctly. The jacket and pant layers won't show in game. Can you fix this?
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The reason this is happening is that the way the jacket layer is rendered in-game is very weird and AFAIK not officially documented.
I've researched it and discussed my results here.
If you compare that "helm map" (or jacket map, or whatever) to your skin file, you'll notice that the green (body), red (right leg), and blue (left leg) areas have no transparent pixels, while the three others (head, 2 arms) do have them. That's why the jacket layer shows up on your Head & Shoulders™, but not on your body or legs.
To fix it, you'll have to place at least one transparent pixel in each of those boxes, but it's best to make everything transparent apart from the actual parts used as skin.
What's wrong with it?