Before 14w29a I used this automated furnace:
[ ][C]
[C][H]
[H][F]
[ ][H]
[ ][C]
Where:
[C] - chest
[H] - hopper
[F] - furnace
I used it for large amounts of cobblestone or clay. As fuel I used Lava Buckets loaded to the left chest. When lava from bucket was used by furnace empty bucket drops to the chest via hopper.
But after 14w29a this mechanics was broken and now empty bucket stays in the fuel slot of the furnace. See the pictures.
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I can confirm that the bug is still here in 14w30c. Even in a more minimal setup where the furnace is manually filled with a bucket of lava (or an empty bucket) as fuel and with some combustible, the hopper underneath isn't able to retrieve the empty bucket. It does however still retrieve the smelted materials.