The story's download counter counts accesses by readers during log in periods. That means that when a reader accesses a story today, that counts as one story access on their account and the story's download counters (daily, weekly and global) are incremented. If the same reader accesses the story again during the same day, their counter is not incremented, neither are the story's counters.
However, if the same reader accesses the story again the next day, then all counters are incremented; the reader's and the story's.
Chapters have download counters too, but those work differently. Due to the large number of chapters on the site and the large number of users, it becomes somewhat impossible to track who accessed what during a log in period. So due to this lack of tracking, chapter counters are incremented all the time. So if a reader accesses a chapter and then clicks the reload button on their browser, the chapter's counter gets incremented again while the story's counter doesn't.
Another issue must be taken into consideration is the navigation hints in stories. The site started using navigation hints in the form of <LINK rel="next" ...> in July of 2013. Some browsers like firefox and Google's Chrome, when they see these links they prefetch the file they point to in order to speed up browsing. So whenever a reader clicks on the link for a serial story, the site usually sends the index page, and the index page contains a "next" link to the first file in the story, be it a foreword, chapter 1 or prologue. And thus the browser that prefetch pages will hit those first files right away, whether the reader click on that first part or jumps to the last part of the story. So the first parts of every multi-part stories will ALWAYS have abnormally high download counts. That high number doesn't mean anything. It's just not easy for the system to discount those extra download hits because they're occurring whether the reader sees the downloaded file or not.
These differences between the way downloads are counted for stories and for chapters makes the correlation between story download counts and chapter download counts impossible.