Comparing this item:

To this one:

with item.equals(otherItem) returns false, whereas the items are literally the same, the only thing that changes is the order of the tags in its lore NBT representation.

The problem is that when comparing two CraftItemMeta, it compares the lore of the two metas not as NBT compounds, but as Strings, so even if the NBT are the same, the String are different and comparing leads to false value.

Sorry if I'm not really comprehensible :/