We have the analytics code in the footer for sure. When I view the source it is the last thing before </body></html>. I know that the footer template is not working properly because I have added in a comment <!-- test test --> but it won't show up in the source on the index page, just isn't there. I have tried searching for the analytics code with the search in templates section but didn't find anything. I searched in the DB and same thing. Its just not there.
I only have 1 style too so it can't be me updating a different style.
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