Furnaces will only smelt items when there's a flammable item visible in the correspondent slot.

(For snapshot "22w12a")

If you wish to cook/smelt an item, the furnace now requires there to be an item burning even if the furnace is using the "heat" from the previous one. For example: if you use lava buckets to fuel your furnaces, if you take the bucket out and don't replace it with any other item, the smelting progress would stop.