diff -u b/core/modules/system/system.install b/core/modules/system/system.install
--- b/core/modules/system/system.install
+++ b/core/modules/system/system.install
@@ -435,6 +435,15 @@
   if ($phase == 'update') {
     $profile = drupal_get_profile();
     $files = system_rebuild_module_data();
+    // Build dependencies based on non-system_info_alter-ed info files
+    // if we are fired before the alter could even run.
+    if (drupal_get_bootstrap_phase() < DRUPAL_BOOTSTRAP_CODE) {
+      foreach ($files as $record) {
+        $record->info = $record->parsed_info;
+      }
+      $files = _module_build_dependencies($files);
+    }
+
     foreach ($files as $module => $file) {
       // Ignore disabled modules and install profiles.
       if (!$file->status || $module == $profile) {