I started minecraft laucher and i noticed there is new 1.9.4 update. I tested it in vanilla. I was on my little server but then i noticed there is something wrong in my skin. I thinked it was just server but i tested it in other server and in singleplayer. it was almost white. It was normal in 1.9.2. i put here my skin file if that helps.
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The second layers have existed since 1.8 (head since start) they just fixed an issue where they don't render under certain conditions.
This is the intended behavior. Your skin is fully opaque white and is rendering fully opaque white.
Pre 1.9.4, some magic was done on all skins to make fully opaque areas not render at all. This was highly confusing as skin makers couldn't make fully opaque skins without running into problems. This was kept for compatibility with very old skins without a second layer (32x16 pixels).
The magic was removed for modern skins (32x32). If you don't want part of the second layer to render, turn it off in the options or make your skin with a transparent background.
The clothes layer isn't transparent, make it transparent to fix it. If you don't know about the clothes layer, then go look it up.