Putting a single Configuration 1 circuit into the Blast Smelter produces either Molten Terrasteel (if EnderIO compat. is enabled) or Molten Pulsating Iron (compat. is disabled).

Using the latest GT++ version compiled from GitHub.

Enabling debug mode in the config and looking at the logs, it seems the Phased Iron recipe loads before the Terrasteel recipe. I'm guessing disabling the compat makes the Phased Iron recipe error first and skips the rest of the errored recipes.

Sidenote: Every recipe from Botania (Terrasteel, Manasteel, Elementium) seems to error.

What GT version are you using?

Using the latest GT version compiled from Github (July 22nd)

I don't see how the enderio config changes the output.