... Oh. What probably happened is you edited Nauvis, thinking it was settings for all planets. You added Scrap (and everything else) to Nauvis. Only Scrap generated, because the others only work in their biomes. (I don't fully understand this last part.)
There is no way to edit settings for all planets after map generation. You edit one surface at a time. I would just not put Scrap on Nauvis unless you're doing it on purpose. Leave the box unchecked.
I will try putting the planet's name on the right panel to make this more obvious. But it is just how the mod works. /editor has the same limitation.
