When using the /enchant command, it uses string ids for enchanting the current held item; for example:

/enchant @p minecraft:efficiency 3

However, the ench NBT tag still uses the old numerical ids; for example, this doesn't give efficiency, but instead gives protection:

/give @p minecraft:diamond_pickaxe 1 0 {ench:[{id:"minecraft:efficiency",lvl:3s}]}