Sounds to me like the problem you will likely be trapped in is the pwd of the executing directory. Using a relative include no matter what script its defined in will always work relative to the pwd of the executing script. So with this, dd is located under /dd, which included /dd/dda.php, which in turn includes /includes/*.
Since you mentioned .., this would indicate relative. Use this for your inclusion within dda.php:
etc. You can use whatever inclusion type you want.
require_once dirname(__FILE__) . '/../includes/header.include.php';
Now when you include dda.php into dd.php, whether you pull from the dirname or not the inclusion within the dda.php will resolve relative from /dd, and not from /.