Creative mode, new world, 13w04a
I can reproduce this about 1 in 6 tries by having a hopper load coal into a furnace then shift clicking ore into it. The furnace is off with full coal, and when I load ore the hopper loads another coal, the furnace window closes and everything in the furnaces inventory disappears.
edit: This happens in survival and creative. Still occurs in 13w04a.
It only crashes the furnace interface, i forced a crash to get a report in a newly generated world. Nothing in it but the furnace the hopper attached to its side and 64 coal in each. The interface crashes right when any ore is shift clicked into the furnace and the ore and coal in the furnace disappears.