mods.enderio.AlloySmelter.addRecipe(<metallurgy:damascus_steel_ingot>*3, [<ore:ingotBronze>*2, <ore:ingotIron>]);

Will ignore the '*2' and register as: 1 bronze + 1 iron -> 3 damascus steel

However, if I use specific IItemStacks for the input like below then it works fine

mods.enderio.AlloySmelter.addRecipe(<metallurgy:damascus_steel_ingot>*3,[<nuclearcraft:alloy>*2,<minecraft:iron_ingot>]);

I can work around this obviously, but it is a bug

This appears to be a bug in CraftTweaker. When converting an IIngredient with a count to a normal Ingredient, it discards the stacksize. I've mentioned it to them, so hopefully they resolve it quickly.