Why are my PDFs sorted differently in Bookshelf or Titles view?

I scanned 68 chapters of two med textbooks (2000 pages) so I can access them easier on my iPad.
It works OK but there is one odd thing-after dragging the chapters to iTunes and syncing them, I get different sort orders for the "Bookshelf" view and "Titles" view depending on if I am in ICON mode or LIST view mode (top upper right)
The chapters are each named 01.pdf, 02.pdf, 03.pdf, etc etc.
If I look at them in "List" view, with the TITLES button selected they are all sorted from 01-68 properly.
If I look at them in "List" view, with the "BOOKSHELF" button selected, they randomly populate the bookshelf from top to bottom.
This is the same when I view them in ICON mode. They are all out of order.
I know I can drag them around to re-arrange them, but this is a real pain.
Also- I can't just choose "TITLES" and then click ICON view, it reverts to "Bookshelf view"
I was planning to put more textbooks in. A lot more.
What causes them to be sorted randomly when they are in "Bookshelf" view?
I would like to find a way around this so I can either re-name them properly or adjust whatever meta-data (if anything) is causing this.

Unfortunately this has been an issue with iBooks since day one. Bookshelf view has never been sorted alphabetically. Hopefully in a future update this issue will be resolved...
I personally gave up on iBooks for PDF files because of the inability to sort the Bookshelf view with any consistency. I'd recommend looking into the Goodreader app for storing your PDFs. With Goodreader you can create folders within the app for each book and they will sorted in proper order.

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