Ok. . . this is really strange. On a hunch I grew iron essence through Magic Crops and got enough essence to make iron ore.
That ore works in the smeltery.
The ID is 15 (the one that smelts fine from Magic Crops)
The ID of the ore that doesn't smelt (except in vanilla furnace) is 15:8
Not sure that helps. Seems, so far, to only be iron that won't smelt.
There seems to be something really wrong with mine-/modtweaker...
The only thing I can currently think of is the script files being damaged/corrupted...
Can you try the /mt reload command again and give me the minetweaker.log afterwards? (Copy the log file before exiting the world/game; it can be found in the minecraft folder)
Otherwise you can try reinstalling the pack (backup your world saves first!) that should fix it.