please do not edit the default theme Twenty Thirteen directly, but either create a child theme http://codex.wordpress.org/Child_Themes for the customization, or for only formatting, use a 'custom CSS' plugin http://wordpress.org/plugins/search.php?q=custom+css
as @Andrew already hinted at, the problem does not show if one replaces your CSS with the one of an unedited theme (done with Firefox' web developer add-on).
as is, it is too complex to identify how your edits have changed the formatting and caused your problems.