First I was a little bit confused, that skins on player skulls not working:
https://bugs.mojang.com/browse/MC-62964
The inventory shows a normal head (without skin)

The solution:
*Place the skull
*Destroy it
*Collect it

If you give you a player skull over command (not placed before) and put it into the helmet slot all items and strings in the inventory vanish.

If you place the player skull, destroy it, collect the skinned one all works great.

Same in creative mod ...
also water disappear ...

related:
MC-58512
MC-59100