Is black hole and stone rain just exceedingly rare?
 

I've made over 200 new saves and scanned for stone rain and black hole. Neither has appeared a single time, yet pretty much everything else I've searched came back multiple times, so that kind of rules out the scanner being at fault I would think.

Did I just get the names wrong, and they aren't called stone rain or black hole in the US version? I don't see the point of adding new spells if no one will actually ever see them.

Edit: Actually, I just found the code that fills up the spellbook with all spells at rank 1. Yep, both of those spells are still named that, and they still have yet to appear legitimately in any of my saves.
Grrr...

Those spells never appear in game on their own. Black hole is reward for clearing basement in castle on Nameless island, and Stone rain is also reward for some quest in game, cant remember but both are 100% sure to be in game. You need to do something to get them, NOT find them.

Well that's helpful, thanks. I was wondering if it was quest related, but some of the quest reward spells were showing up in the scan (i.e. Souldrain).

Yeah, but all these spells (that are Legend abilities turned into spells) are now quest rewards. Save for Turn Back Time, of course.