If you are not using the "view list" then the reading list plugin cannot affect the sorting. Not directly at least. It can only affect the sorting — indirectly — by updating columns that are in your sort order. And the books going to the bottom are probably just following the sort order defined by your view.
If you apply a new view that does not include the following columns: ( On reading list, reading lists ) the books will probably stop going to the bottom.
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