I found a bug in the furnace. If it is connected to the comparator and load ore, the ore disappears and when trying to open the GUI, it closes instantly.The ore does not wind up in the bottom hopper, it just vanishes. Still present in Snapshot 13w06a.

MOD EDIT: Furthermore, the furnace will continue to look like it is burning for the amount of time it should be burning. The hoppers seem to be unrelated to the issue - simply place a comparator behind the furnace and manually smelt the ores. The same bug will occur.