Index: domain_admin.inc
===================================================================
RCS file: /cvs/drupal/contributions/modules/domain/Attic/domain_admin.inc,v
retrieving revision 1.29.2.9
diff -u -r1.29.2.9 domain_admin.inc
--- domain_admin.inc	25 Jul 2008 17:50:45 -0000	1.29.2.9
+++ domain_admin.inc	29 Aug 2008 00:31:50 -0000
@@ -277,7 +277,7 @@
       This feature requires the hook_url_alter() patch.')
   );
 
-  $options = array();
+  $options = array('-1' => t('Do not change domain'));
   foreach (domain_domains() as $data) {
     // The domain must be valid.
     if ($data['valid']) {
Index: settings_custom_url.inc
===================================================================
RCS file: /cvs/drupal/contributions/modules/domain/settings_custom_url.inc,v
retrieving revision 1.1.2.3
diff -u -r1.1.2.3 settings_custom_url.inc
--- settings_custom_url.inc	25 Jul 2008 17:50:45 -0000	1.1.2.3
+++ settings_custom_url.inc	29 Aug 2008 00:29:28 -0000
@@ -96,7 +96,7 @@
         }
         // If strict SEO rules are enabled, we set "all affiliate" links to the root domain.
         // Only needed if we are not on the default source domain.
-        else if ($seo && $_domain['domain_id'] != $root['domain_id']) {
+        else if ($root != -1 && $seo && $_domain['domain_id'] != $root['domain_id']) {
           $absolute = TRUE;
             // In this case, the $base_url cannot have a trailing slash
             $base_url = rtrim($root['path'], '/');