I'm using a Cauldron server with Multiverse plugin to have multiple words. Each user has a separate inventory, for creative and survival. The inventory is stored and loaded by another server plugin called LimitedCreative (https://github.com/possi/LimitedCreative).

After an inventory has been stored and loaded, all Botania flowers revert to "Botania Flower", saying "If you have this, it means something went wrong, you should report it".

Example of data stored in .yml files:

inv:
'0':
==: org.bukkit.inventory.ItemStack
type: BOTANIA_SPECIALFLOWER
amount: 21
'1':
==: org.bukkit.inventory.ItemStack
type: BOTANIA_SPECIALFLOWER
amount: 3

Some items show meta data (enchantments e.d.), the flowers don't..

Cauldron server with Multiverse plugin

That's your problem. It doesn't save NBT.