Ok, I have NO clue why this worked, but it did so I'll put it here in case anyone else runs into this issue. Every time I failed to save Naomi what I would do is select her, select “Find an item to stand on” and then leave the room and come back in. I didn't even know you could leave the room without selecting an option at all; but I just found out, didn't select her at all, and instead left the room and came back in. And then I proceeded exactly as I had every other time.
And it worked. Now I have no idea why this would work, or if it was even the catalyst. But as it was the only thing I did differently than every other time I can only assume it was the cause ridiculous as that might be. So there you go in case this comes up for anyone else.
Also, thank you for all the responses.
Jacqli - Ar Tonelico 2
Better than every character, ever. I will hear no contest!...because you would be wrong.