What I expected to happen was...:
I started over with the template of https://minecraft.net/profile ( https://minecraft.net/images/3px_reference.png ) and set up the second layer of the skin of Alex with PNG format, and expected to the second layer appear.

What actually happened was...:
However, 2nd layer of the skin of Alex does not appear as I set up.
I attached the skin data with PNG format and snap shot of Mincraft for your reference.

Steps to Reproduce:
1. Downloaded template of the skin of Alex with the template of https://minecraft.net/profile ( https://minecraft.net/images/3px_reference.png )
2. Modifed the template by using Paint sof, saved in PNG format.
3. Uploaded the file to the profile page of Mincraft.
4. Launched Mincraft.
5. First layer of the skin propperly appeared but second layer did not.
6. I selected "skin customize" option "on" in the menu of MIncraft.