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The only other thing that I can think of that might be affecting the sort order is a book ID. Calibre does have them associated with each book, but they're hidden. You can find them in the Book Viewer (the window with book info, not the thing on the right of the book list). Perhaps somehow your ereader is using that field as the primary sort order? But this seems like an unlikely situation inside calibre.
Oh, the viewer I'm talking about is on the context menu after right-clicking on a book in the book list, about halfway down.
(In case you don't see the ID's in the Viewer, you might need to turn on the fields in Preferences.)
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