Messes up book hierarchy

I have about 340 nodes in one big book.
The book has about 15 top level pages and these all have children. The maximum depth is 5 levels.

I set up a view for this using the method on https://www.drupal.org/node/1493366 → .

It kind of works but, for some reason, it sort of gives up creating the tree at a certain point.
It misses some of the 2nd level book pages, but the child pages of this are intact and show in random places as top level pages.

In the book outline the structure is intact, but views tree for cannot make sense of it.
Sorry I do not understand what is going on.

Any notion as to why it might be doing this?
I know this is really vague, but I am stumped on this.