What settings from a zen sub theme are not saved as files? Im duplicating a zen sub theme so that I can later modify the styling. Ive duplicated the theme folder and changed its name. Ive changed the .info file name, and ive changed the theme name for theme overrides in my template.php and theme-settings.php.

When I enable the new theme its very much like the old one but there are still some differences. Ive looked at the theme settings pages in drupal and applied the settings from the original theme to the new one, but there are still some differences. 

What other settings to do with the theme would not have been copied across with the files and also arn't visible on this page? 

The only module that Ive found that I think could be affecting the layout is Panels which controls a couple of pages. Ive changed the selection criteria from themeA to themeB so I dont think its this module causing the difference.
There are two major locations for theme configuration - be it a sub theme or a primary theme:


http://example.com/admin/appearance/settings/yourtheme


For a zen sub-theme, this page lets you configure display of logo, site-name, slogan, and more, including a couple of menus. Also the favicon (shortcut icon), breadcrumb settings, and more can be found here. 


http://example.com/admin/structure/block


You need to configure each block's "Region Settings" (click "configure"  on the right), to assign or adjust a region for the block to your new theme. The region settings provide a pull-down menu with available regions for each enabled theme. 

If you want to duplicate settings from one sub-theme to another sub-theme, make sure you adjust all files in the theme folder (theme.info, template.php, theme-settings.php). If you do extensive theme pre- or post processing, and change themes frequently, you might want to roll these into their own custom modules (see How to modify module output via another module - whois module? for an example of the same functionality as theme pre-processing or custom module). 

There might be additional settings in contributed modules - you mentioned panels.