Just wanted to tell you. First of all I can't craft weapons or tools out of the metallurgy ingots and second is that I for example melted down Vyroxeres Ore and got Shadow Steel Ingots instead of Vyroxeres Ingots.
Grrr, same problem here. Smelted Sanguanite in Tinker's smeltery and got Ignasium. Fix please, need my tinker's tools.
Update to this: I did some testing on the Metallurgy Nether Ores in various machines and it seemed to be that all Ender IO machines kept the ores straight through the process. I used SAG Mill to turn it into dust and the Alloy Smelter on 'Furnace Only' setting and got the corresponding ingots to the original ore blocks. I haven't tested every single one but after several different ones coming out correctly I was convinced. I hope you can utilize this! Mine on my friends.