diff --git a/includes/bootstrap.inc b/includes/bootstrap.inc
index a5a7d5d8b2e6e9b8f5397b074adfe6aa8fffdf0a..cda1bb8b81e1f3babb9e65de7043f370771de982 100644
--- a/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -1388,6 +1388,9 @@ function drupal_anonymous_user($session = '') {
  * @param $new_phase
  *   A boolean, set to FALSE if calling drupal_bootstrap from inside a
  *   function called from drupal_bootstrap (recursion).
+ * @return
+ *   The most recently completed phase.
+ *   
  */
 function drupal_bootstrap($phase = NULL, $new_phase = TRUE) {
   $final_phase = &drupal_static(__FUNCTION__ . '_final_phase');
diff --git a/includes/theme.inc b/includes/theme.inc
index ca0e533aa77828e18091f32d87cd2f8bfa84ce54..736662db6a8694294bb7c457558487a85dcd770c 100644
--- a/includes/theme.inc
+++ b/includes/theme.inc
@@ -251,13 +251,18 @@ function _theme_load_registry($theme, $base_theme = NULL, $theme_engine = NULL)
   $cache = cache_get("theme_registry:$theme->name", 'cache');
   if (isset($cache->data)) {
     $registry = $cache->data;
+    _theme_set_registry($registry);
   }
   else {
     // If not, build one and cache it.
     $registry = _theme_build_registry($theme, $base_theme, $theme_engine);
-    _theme_save_registry($theme, $registry);
+   // Only persist this registry if all modules are loaded. This assures a 
+   // complete set of theme hooks.
+    if (drupal_get_bootstrap_phase() == DRUPAL_BOOTSTRAP_FULL) {
+      _theme_save_registry($theme, $registry);
+      _theme_set_registry($registry);
+    }
   }
-  _theme_set_registry($registry);
 }
 
 /**