Someone had started a thread about coloured text not showing up in inventories opened using plugins. Whilst looking through the source I saw the following line:

player.playerConnection.sendPacket(new PacketPlayOutOpenWindow(container.windowId, windowType, new ChatComponentText(title), size));

Whilst the open window packet does support coloured text (it is a Chat field and not a string field), the text gets directly inserted in a new ChatComponentText instead of first parsing the old chat format (paragraph sign + code) using the already available methods in Bukkit! This code is stated in:

CraftHumanEntity#openCustomInventory(Inventory, EntityPlayer, String)

The fix is by changing that line to something like the following:

player.playerConnection.sendPacket(new PacketPlayOutOpenWindow(container.windowId, windowType, CraftChatMessage.fromString(title)[0], size));