With the new addition of second layers for the entire skin, there is a bug when you enter a portal. If you have your second layers toggled On, when you go through a portal they will appear to be Off, despite still being On in your settings. This happens from Overworld to Nether, and from Nether to Overworld, and can only be fixed by toggling one of the second layers, or by logging out and back in again. However, this is only client-side.
Linked issues
is duplicated by 5
MC-45103
Jacket layer disappears after going through portal
Resolved
MC-45110
New skin system resets after switchin from overworld/nether/end
Resolved
MC-45230
if you go into the nether you loose your skin hat
Resolved
MC-45295
Nether & End removes skin layers and capes
Resolved
MC-45636
When going through nether portal Hat dissapears.
Resolved
Still in 14w04a