If you use table prefixing (http://drupal.org/node/2622), to make tables that are in the same physical database as your Drupal installation but are not part of it (i.e., are not prefixed) available to Table Wizard, you need to add the database as if it were external:

$db_url['default'] = 'mysqli://root:pass1@localhost/drupaldb';
$db_url['defaultnotdrupal'] =   'mysqli://root:pass1@localhost/drupaldb';

When using external tables in a table prefix environment, Drupal will prefix the external tables by default, which in most cases is not what you want. To get around this, you can set empty prefixes in settings.php for the external tables you are using:

$db_prefix = array(
  'default' => 'pf1_',
  'externaltbl1' => '',
  'externaltbl2' => '',
);