Parts in the header and footer are being overridden by the magento blank theme.. ie. logo and newsletter signup in the footer.
I looked in the DB under the theme table and everything is identical to our production environment after upgrading a lower (staging) environment.
Looked for the value to be correct and not virtual.
select * from core_config_data where path like "%design/theme/theme_id%";
Everything seems to be matching production. All i know at this point is when i did the upgrade somehow the magento/blank theme is overriding certain elements.