It's a simple issue, the InventoryType.BREWING is still defining that brewers have 4 inventory slots instead of 5.

Minecraft added a fuel slot to brewing stand on 1.9.

This makes impossible to change the fuel in custom inventories of this type.

If we attempt to copy the inventories from a real brewing stand it will also fail because the custom inventory size is 4.

customBrewingInventory.setContents(realBrewingInventory.getContents());

java.lang.IllegalArgumentException: Invalid inventory size; expected 4 or less
at org.bukkit.craftbukkit.v1_9_R1.inventory.CraftInventory.setContents(CraftInventory.java:65)