Re-tested in latest version and latest snapshot, this is still an issue. Moreover, it appears to be an issue when exiting and reloading the game.
You can resolve the issue by relaying the one row of hoppers, the issue will no longer be there for the duration of your play, however on exiting and reloading, the issue will return.
For the furnace distribution system in question, this means I need to replace 9 hoppers every time I want to distribute coal between my furnace array each time I use it. Not a massive inconvenience, but still an issue nonetheless.
Thanks for your detailed analysis, Doug. Apologies that in the original issue raised, every time I noted the 'third' furnace being the broken one, it was actually the 'fourth' being broken, thanks for pointing that out.
I used scenario c in your above list to resolve the issue, however replacing the hoppers above 2 and 3, while fixing the issue with furnace 4, creates an issue with furnaces 1 and 2. You don't notice this issue with a stack of 8, however if you use 16 fuel, furnace 1 gets 3 fuel, furnace 2 gets 1 fuel, and the rest get 2 fuel. This difference increases with larger stacks, essentially furnace 2 only gets 1 fuel (the last to be dropped), and the rest are distributed evenly.
Note that all problems go away when you replace the entire row of hoppers at the same time; I just tried this then added 8, 16, 40, then 5 stacks of fuel consecutively, checking each amount distributed properly.
Note that the pulse extender has no bearing on the beginning of the distribution, only the end to ensure that the last 1-8 units of fuel are dropped successfully; without it, the distributor was dropping fuel from the first 2-3 hoppers too quickly when the chest emptied, leading to more items in the first 2-3 hoppers. The pulse extender inputs to an AND gate, meaning that when the input chest has items, the signal immediately switches off, but when it empties, there's an 8-tick delay before outputting a signal again.
Copy-pasting the schematic in a creative or survival map resolves the issue, and now that I've replaced all the top hoppers, the issue is also resolved. It seems the bug here is more a question of the order that the hoppers are placed in, potentially causing varying speeds of input to adjacent hoppers. My guess is that if you place the hoppers in order 1, 2, 3, 4 then there is a consistent speed, but if you place in the order 1, 3, 4, 2 there is a fractional reduction or increase in speed to hopper 2.
My current guess is that hopper inputs/outputs work on a BUD mechanism which perhaps bugs out if you place blocks in a non-uniform order, then applying a uniform redstone pulse to the hoppers doesn't communicate well with the BUD.
Hi Alex, this is still an issue that has not been resolved or looked at. Sorry, I don't have the time to retest in every single snapshot. My current workaround is to clear down a row of hoppers and replace them any time I want to use my industrial furnace. The bug reappears on logging out and back in to a game or unloading and reloading the chunk.