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If the eyes are black, it's probably because the area of the texture which covers the eyes is white on your alpha channel. Any part of the texture with a white alpha will show up as part of the makeup, whereas any part with a black alpha will be invisible, showing the regular skin or eyes underneath. It could also be that you selected DXT1 when saving - you'll need to use DXT3 or DXT5.
Do you know how to get to the alpha channel? Which graphics program are you using? Which modding program are you using -
CTU or TSRW?
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