I set up an auto loading and unloading furnace using hoppers, a furnace, and a chest. I found that when using lava fuel, the bucket doesn't go through to the output hopper correctly. I am on 1.5.1 playing on a private server with no mods.
Configuration:
Left - fuel hopper
Top - raw material
Bottom - finished material, piped to a chest via hopper
Attached you'll find screenshots.
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Unable to reproduce. Make sure the server is running 1.5.1.
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How do you check the server version without mod privileges in game?