Helen is correct. Books are only added to the read count if you finish it. All you have to do is somehow get to the last page of the book and turn the page.
The read count is taken from the Event table. It is the count of rows with EventType=5. When you finish the book, the row is added for the book, or if it already exists, the EventCount on the row is incremented.
The Kobo Utilities plugin won't help with this. It marks the books as finished in the content table, but it isn't doing anything with the Event table. I doubt if this will change as there is data in the row that I don't know how to create.
If you really want to get them in sync, the following query will find the books that you need to finish:
Code:
SELECT *
FROM content c LEFT OUTER JOIN Event e on c.ContentID = e.ContentID
WHERE ReadStatus = 2
AND ContentType = 6
AND EventType IS NULL
You can then open and finish each of these books.
From memory, a side affect of this is that if you delete a book, the above Event row is not deleted. That means, the device tells you how many books you have read and finished. But, the percentage finished is the count of books currently in the library that have been marked as finished.