Bone charm traits not carrying over?

So I destroyed all of my bone charms at the end of my first run, because the screen when you click on NG+ said they'd carry over. I know that the physical ones do not, so I sacrificed them, but they don't show up in my new game.

Here the game says I have a whole bunch of traits I can use (most are from my last run)

Yet here it shows I don't even have 20. And all of those were from this run.