If I am not mistaken the "Aetherium Ore" you mentioned is from this mod: http://skyrim.nexusmods.com/mods/23530//? To smelt them into ingots, you are supposed to use Aetherium forge before completing the quest. There seems to be some incompatibility issues so sometimes when the quest is complete, you lose the smelting options. I personally have experienced quiet a bit of issues with the mod so eventually I decided to remove it from my archive. If you so desperately need the ingot then I suggest you acquire them via console.