Ever since the CC update before the latest one my slideshow has had this odd timing issue. It is setup properly in the settings for 5000ms but will pause for a decent amount of time at the second article. It will eventually change but takes much longer than the first change.
I have the same problem since upgraded to WP 3.6
See this post, the explanation to the problem of slideshow is below, in the comments… custom-community-update-1-17-3