diff -u b/core/includes/bootstrap.inc b/core/includes/bootstrap.inc
--- b/core/includes/bootstrap.inc
+++ b/core/includes/bootstrap.inc
@@ -1090,6 +1090,7 @@
  */
 function bootstrap_invoke_all($hook) {
   foreach (module_list('bootstrap') as $module) {
+    drupal_load('module', $module);
     module_invoke($module, $hook);
   }
 }
diff -u b/core/includes/module.inc b/core/includes/module.inc
--- b/core/includes/module.inc
+++ b/core/includes/module.inc
@@ -30,7 +30,7 @@
   static $has_run = FALSE;
 
   if ($reset) {
-    $has_run = FALSE;
+    $has_run = !$bootstrap;
   }
   // Unless $boostrap is NULL, load the requested set of modules.
   elseif (isset($bootstrap) && !$has_run) {
@@ -149,7 +149,7 @@
       // drupal_get_filename() static cache for bootstrap modules only.
       // The rest is stored separately to keep the bootstrap module cache small.
       foreach ($lists['bootstrap'] as $module => $filename) {
-        _system_list_warm('module', $module, $filename, TRUE);
+        _system_list_warm('module', $module, $filename);
       }
     }
     else {