I thought I was crazy, but I made a bolt at the beginning out of wood and iron and feathers. I upgraded it with enderium tipped slimeleaf rod, and the damage was the same. So I created a new bolt out of the same material, and the damage was out of this world! Same materials, but when upgrading bolts, the damage values aren't updating, so you end up with iron damage values on something that should have Enderium damage values.