you have to finish the level with skull in hand

there are silver skulls and gold ones
silvers skulls don't give you achievements
gold ones do and you don't need to finish the level.

you do not have to finish the level with the skull
the skull on top of the rails is a gold skull(black eye) you must be thinking of the Grunt
Birthday party skull after you fight the chieftain

i would suggest you start the level over
another reason yu might not get the achievment is because u already got it