Randomly furnaces delte all containing items while smelting, keeping the furnace in the active state.
I'm using hoppers to fill the furnace with items and fuel (top/side) and to get the smelted items out of the furnace (bottom).
After adding fuel and items through the hoppers they start smelting as supposed but randomly at some point the furnace deletes all items in it, leaving it active. This happens in single player and multiplayer, independent of creative or surival.
This Bugs happend for me since I started using the snapshots with version 13w09c and still exists after updating to 13w10a which should include an patch for some bugs with furnaces.
Because it isn't always happening I wan't able to get much more detail about the bug. However I was mainly using blaze rods in the furnace as fuel and different items to smelt if this changes things.
The screenshot shows my setup I did in creative Singleplayer to try automating furnaces and is the setup I noticed it first. The setup in my surival Multiplayer is pretty much the same but it also happend with just two furnaces and hoppers connected to them.