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What skin element are you making? Perhaps it's one that doesn't support transparency?
FYI, if you import a transparent PNG or use a transparent TGA, you need to make sure both the transparency and translucency boxes are checked. For a BMP with magic pink, only check the transparency box.
This is how I do it....
Start with your image on a completely transparent background. Go to Image -> Mode -> Indexed to set it to indexed color (set the Matte to none if it isn't already). That will eliminate any antialised edges. Then switch the image mode back to RGB, add a new layer in the background, and fill it with magic pink. Then, save that as a BMP.
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