That style of smelter doesn't work well on a Spigot server like ours. Spigot's hopper timings are not the same as vanilla. Vanilla Minecraft moves one item between hoppers each tick, meaning that you can synchronise them all with Redstone. For performance reasons, Spigot tends to move the items a few at a time, and less frequently. It's all at the same general rate, but it's not synchronised to the redstone ticks in the same way.
The end result being if you build that type of furnace array on our server, then each time the system pulses, some of your furnaces will get more than one item while others go empty.