Index: modules/system/system.admin.inc
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.admin.inc,v
retrieving revision 1.270
diff -u -p -r1.270 system.admin.inc
--- modules/system/system.admin.inc	24 Apr 2010 14:49:14 -0000	1.270
+++ modules/system/system.admin.inc	26 Apr 2010 05:10:04 -0000
@@ -1240,7 +1240,6 @@ function system_modules_submit($form, &$
   registry_rebuild();
   system_rebuild_theme_data();
   drupal_theme_rebuild();
-  cache_clear_all('system_list', 'cache_bootstrap');
   node_types_rebuild();
   menu_rebuild();
   cache_clear_all('schema', 'cache');
Index: modules/system/system.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.module,v
retrieving revision 1.923
diff -u -p -r1.923 system.module
--- modules/system/system.module	24 Apr 2010 14:49:14 -0000	1.923
+++ modules/system/system.module	26 Apr 2010 05:10:05 -0000
@@ -2173,6 +2173,11 @@ function system_update_files_database(&$
     }
   }
   $query->execute();
+
+  // If any module or theme was moved to a new location, we need to reset the
+  // system_list() cache or we will continue to load the old copy, look for
+  // schema updates in the wrong place, etc.
+  system_list_reset();
 }
 
 /**