Certain Mob textures do not take to the HD Textures and show up white
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is duplicated by 5
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Like I said in my first comment, take the eyes overlay file (the one that "glows" in the dark) and make the background (everything you have transparent now) black. How the blending works, black will show up as invisible. Default textures don't do it because how it is indexed is very odd, and might have the "background color" of the image (a property of the image, not the image itself) set to black. If you un-index the default eyes files from default, and try to use them, this problem will happen. Making the background black fixes it.
This is NOT an error caused by HD textures. It is a blending error with the glowing eyes file (for example, enderman_eyes.png), if you un-index the file (even if you re-index it), you need to give it a black background or else the mob will turn white.