When you give an item with the exact same NBT Data as you already have in your inventory, the items do not stack, only after logging out and back in.

How to reproduce:
-execute:

 /give @p 1 1 0 {ench:[{id:1}]} 

-log out and back in
-execute:

 /give @p 1 1 0 {ench:[{id:1}]} 

-the items do not stack
-log out and back in
-the items now stack

Notes:
-This problem existed before using renaming stuff in an anvil MC-5413
-You do not always have to log out and back in sometimes waiting a few seconds also works