When you set scoreboard like:
/scoreboard objectives add mea dummy
and add it to entities within save area of structure block:
/scoreboard players add @e[type=!Player] mea 3
than you save area with this entity and load it, pasting the same command as above:
/scoreboard players add @e[type=!Player] mea 3
will show that one entity has mea=6, but second started from scratch: mea=3.
There is exception of this for scoreboard tags stored in entitydata (which is very useful).

EDIT: It might be intended, because scoreboard objectives, except tags, are per world, not stored in the entity.