It seems that automatic deconstructor doesn't work on furnaces of any kind (stone, steel or electric). I get an error message followed by the red X on each of the furnaces, i.e., the vanilla indicator that an object has been marked for deconstruction.
Check if the furnaces are not in the middle of crafting, the mod detects whether there are items inside furnaces, so you will have to pick them up manually so items don't dissappear.
