Index: includes/common.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/common.inc,v
retrieving revision 1.756.2.32
diff -u -p -r1.756.2.32 common.inc
--- includes/common.inc	3 Dec 2008 12:33:11 -0000	1.756.2.32
+++ includes/common.inc	7 Dec 2008 16:12:23 -0000
@@ -3632,7 +3632,16 @@ function drupal_flush_all_caches() {
 
   drupal_clear_css_cache();
   drupal_clear_js_cache();
-  system_theme_data();
+
+  // If invoked from update.php, we must not update the theme information in the
+  // database, or this will result in all themes being disabled.
+  if (defined('MAINTENANCE_MODE') && MAINTENANCE_MODE == 'update') {
+    _system_theme_data();
+  }
+  else {
+    system_theme_data();
+  }
+
   drupal_rebuild_theme_registry();
   menu_rebuild();
   node_types_rebuild();