I had the same problem. I was able to delete all the books on my iPod. Then I loaded "zero" books by unchecking them all in the books list on the Books Sync page), and resync the iPod. Once the files were sync'd (and the Bookshelf list was now empty on the iPod), I rechecked the books on the Books Sync page and did another Sync. The "new" books showed up in the categories I had corrected. Mine are set to "Sort by Title" and that's the way they showed up on the iPod bookshelf list.
It should be noted that my "books" are all PDF files, and not purchased books, but I think this procedure may work for you. This is different than the way music syncs, where it reflects any minor change you make to the music list, genre, etc. Hope this helps...Jack
This "nuclear option" solved the problem for now...until I get new books, I guess. I could never figure out which were going to follow the changes in iTunes. There was actually one extra step, only in iOS 6 and higher. I had to go to Settings and turn off "Show All Purchases" in the iBooks settings. Then I waited until iBooks showed that I didn't have any books. In the meantime I checked iTunes to be sure the books were all in their correct sort order, then resynchronized. After about five minutes of resorting, the books were in their final order.
It would be great if I could only eliminate the specific books that are in the wrong place, so I don't have to do this complete replacement every time the books get out of order. Maybe in an upcoming version of iBooks.