Working as intended. Please see the Wiki at http://minecraft.gamepedia.com/Egg#Spawning_chickens
This is probably the high view distance (16) causing a delay whilst chunks are loaded. If you reduce it to 3 or 4, do you see the problem go away? If so, try different values until you find a suitable one.
You may find that the problem will become less severe if you allow the world to fully load before trying to interact with it.
My mistake with the resource pack. 🙂
Seems like the spawn chunks are created (but not rendered) then, when the view distance is increased to 32 the player is dropped into the world exactly at the point the demand for chunk creation (the difference between 10 and 32 view distance) pushes rendering into the background until complete. Might be an idea to force spawn chunk rendering before considering extended view distance requirements. Alternatively, delay world appearance to the player until at least the spawn chunks are rendered then let the rest generate as they do when a player moves through the world.
A view distance of 32 and 512x512 textures is a massive workload. Does the delay reduce with lower resolutions and/or smaller textures?
Your survival map as supplied has furnace 2 with 2 coal and furnace 4 empty. Furnace 3 seems fine. I can reproduce this reliably by putting 8 coal into the chest.
I created each of the following scenarios with a fresh copy of the supplied survival world:
a) If I replace the top hopper above furnace 2 and test, there is no change.
b) If I replace the top hopper above furnace 3 and test, furnace 3 now receives no coal instead of 4.
c) If I replace the top hoppers above both 2 and 3 at the same time, the problem goes away and distribution works as expected.
d) If I replace the top hopper above furnace 2, test, then replace the top hopper above furnace 3 and retest, the outcome is as per b) above.
e) If I replace the top hopper above furnace 3, test, then replace the top hopper above furnace 2 and retest, the problem goes away and distribution works as expected.
It probably works in creative because the hoppers were recreated when you pasted with MCEdit. Have you tried copying it within the survival world? Does it then work?
P.S. The additional redstone circuit with the pulse extender complicates matters. Unfortunately, It allows the first couple of items to drop into furnaces before turning the filters off. This is what causes more than 1 item in furnace 2 above.
If you make the hoppers 3 high instead of 2, the bottom one can take from the filtered hopper without the need for an extra delay circuit. This also clarifies the problem by having 1 item in each furnace except 4 and a second redstone pulse from the last hopper when the item that did not drop into furnace 4 hits the end of the hopper train and drops into furnace 8, IYSWIM?
My apologies. It transpires the server was not a Minecraft vanilla server but a Spigot one. Cannot reproduce on a vanilla MC server. Report withdrawn.