I haven't found the underlying issue/difference yet, but:

With Spigot 1.20.2, loading this item stack from a config file:

item:
  ==: org.bukkit.inventory.ItemStack
  v: 3578
  type: STONE
  meta:
    ==: ItemMeta
    meta-type: UNSPECIFIC
    display-name: §9Test

yields an item stack with this NBT data:

On Spigot 1.20.4, this suddently results in an item with this data instead (causing the item to not match existing items on the server):

Example plugin attached: Command "/test" gives the item loaded from the config file.