This is still a bug in 13w10a. I just tried it with a hopper feeding cobble into a furnace with another hopper taking the furnace output into a chest. The furnace is facing west. After placing the cobble (shift-click) in the furnace and in the hopper I shift-click a lava bucket into the furnace and immediately the furnace interface closes. When I open the furnace again all its contents are gone (cobble, lave, bucket) and it is loading more cobble from the hopper.
This is still a bug in 13w10a. I just tried it with a hopper feeding cobble into a furnace with another hopper taking the furnace output into a chest. The furnace is facing west. After placing the cobble (shift-click) in the furnace and in the hopper I shift-click a lava bucket into the furnace and immediately the furnace interface closes. When I open the furnace again all its contents are gone (cobble, lave, bucket) and it is loading more cobble from the hopper.