Put the summary of the bug you're having here
What I expected to happen was...:
hitboxes and block (skull) should be aligned
What actually happened was...:
hitboxes were centred but render of block (skull) was off centre
Steps to Reproduce:
1. use fill command to fill a row of skulls
2.
3. ...
It is MC-45050 which had been fixed in 14w05a (1.8 snapshot). Apparently, the bug is now the second time in the game!
The problem is that the skulls whose meta key "facing" is either "north", "east", "south" or "west" doesn't render correctly: the model and the hitbox is offset.
Note: using /fill => facing:north is default
Note2: the values "north", "east", "west", "south" aren't currently used. "up" takes it all by containing block entity data to define the actual direction