I wonder if this could be caused by a book that is wedged in the "indexing" algorithm.
If you go to HOME, and search for a nonsense word (xxyyzzy, say) It'll either say "not found" or something different, to imply that some book isn't indexed yet. (I forget exactly what it says.) You could then delete that troublesome book, see if you problem goes away, and re-add the book later for a second try.
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