Hmm, that doesn't sound good. You should only have one scene left to find, and every scene should have at least one other scene that references it.
Is it possible you're missing where 6 is in 12? That seems to be the most common issue others have had.
If not, let me know and I can try and help some more.
(Also, I mean, technically 01-QU, 02-EN and 03-LI aren't referenced by other scenes, but I figure it's unlikely you're missing one of those!)