As of version 1.1.1, this issue still seems to persist. I have no idea the exact cause of this glitch, it just happens randomly.

Hoppers certainly contribute to it, but again it's random, as even with the exact same hopper configuration as a "bugged" furnace, the machine somehow functions as intended. The only TEMPORARY solution I can find to this is to break the furnace and rebuild it.

(Oh yeah, although the "output" hopper briefly shows the item in its slot, the item does not transfer to the chest. Taking out the chest prevents the outputted items from dissapearing. I do believe putting the chest back in could also solve this issue, but since I've "fixed" the furnace AND due to the random occurance of this glitch, I cannot truly verify that statement)