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:
require_once dirname(__FILE__) . '/../includes/header.include.php';
etc. You can use whatever inclusion type you want.
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 /.