We were in the process of requesting a refund for the theme, when we noticed a problem logging into the admin section. The error message said cookies were disabled because of a problem with the header output (the source showed a blank line before the doctype declaration). I enabled wp_debug to display errors, and got error messages that there were problems with the Themeple Shortcodes plugin. I disable it, and was able to login, and the formatting of the front end began working correctly.
I edited the plugin file for the and noticed multiple line returns for the plugin. I used a regex replace to get rid of the extra lines, and it appears that the plugin is working fine now. I don't know if this was an encoding problem with the file, but it did make the entire site not function properly. Changes to the theme options for layout did not change the layout on the front end of the site.
Also, in the file we just downloaded there was no zip file of the theme to upload. Just the folder with the Theme.