diff --git a/drush.php b/drush.php
index a6be5a17b4..00c4e7f6c1 100755
--- a/drush.php
+++ b/drush.php
@@ -38,6 +38,9 @@ function drush_main() {
     register_shutdown_function('drush_coverage_shutdown');
   }
 
+  // Load the Drush configuration files.
+  drush_preflight();
+
   /* Set up bootstrap object, so that
    * - 'early' files can bootstrap when needed.
    * - bootstrap constants are available.
@@ -48,8 +51,6 @@ function drush_main() {
   $bootstrap->preflight();
 
   $return = '';
-  // Load the Drush configuration files.
-  drush_preflight();
   if (!drush_get_error()) {
     if ($file = drush_get_option('early', FALSE)) {
       require_once $file;
diff --git a/includes/command.inc b/includes/command.inc
index f64e9f95f1..b1ddb7405f 100644
--- a/includes/command.inc
+++ b/includes/command.inc
@@ -1060,6 +1060,14 @@ function drush_command_defaults($key, $commandfile, $path) {
     'hidden' => FALSE,
     'category' => $commandfile,
   );
+  // We end up here, setting the defaults for a command, when
+  // called from drush_get_global_options().  Early in the Drush
+  // bootstrap, there will be no bootstrap object, because we
+  // need to get the list of global options when loading config
+  // files, and config files are loaded before the bootstrap object
+  // is created.  In this early stage, we just use the core global
+  // options list.  Later, the bootstrap object can also provide
+  // additional defaults if needed.
   if ($bootstrap = drush_get_context('DRUSH_BOOTSTRAP_OBJECT')) {
     $defaults = array_merge($defaults, $bootstrap->command_defaults());
   }