WitherSkulls instantly revert back to a Rotation of 90, -90 after having their Rotation altered.
Steps to reproduce:
/summon WitherSkull ~ ~ ~ {direction:[],CustomName:"Test1",CustomNameDisplay:1}
/entitydata @e[name=Test1] {Rotation:[0f,0f]}
#Says that Rotation was set to 0, 0
/entitydata @e[name=Test1] {CustomNameVisible:1}
#Says that Rotation is still 90, -90
Using wither skulls directly is not supported and modifying internal data via NBT during the lifetime of an entity can result in unexpected behavior.