I had a reader point out something similar, the second page repeated many of the titles from the first page, leaving out other entirely, even though they are there. Checking with Lazeez, it turns out that this is a known bug in the story sorting mechanism. If you sort the stories by hand, you'll get unexpected results on the second page. He knows it, but has to completely redesign and recode the entire mechanism, so it's sitting on a back burner.
If you're having that problem, your best bet is to simply change the sorting back to alphabetical (just don't "RESET" it, otherwise it trashes your custom order, while if you "CHANGE" it to alphabetical, it'll save it so you can restore it later.
In my case, I wanted to sort my stories by series, so each story would fit under the preceding stories in each series in the correct order. Thus, every time I post a new story, I hand sort the list to get it to come out right. Thus, it won't really hurt if I have to recreate the entire list when Lazeez finally works out a solution. For now, readers will just have to search for the correct story alphabetically.