If you want to use Drupal sessions and the logged in user object from a straight PHP script not at Drupal root but somewhere in subdirectories in a site, you will probably need to do something like I endend up doing in profiles/scf/switch.php to impersonate the Drupal site root directory.
In fact, I think the partial installation profile idea might need something like this.
(Skip down to resolution.)
Some test output code used to figure out what the domains and sessions were doing:
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