diff --git includes/environment.inc includes/environment.inc
index 84a9bd2..9f99fa4 100644
--- includes/environment.inc
+++ includes/environment.inc
@@ -509,9 +509,6 @@ function _drush_bootstrap_drush_validate() {
     return FALSE;
   }
   
-  // Set a warning for Windows users.
-  drush_environment_check_os();
-  
   return TRUE;
 }
 
@@ -616,6 +613,9 @@ function _drush_bootstrap_drush() {
   // Load a custom config specified with the --config option.
   drush_load_config('custom');
 
+  // Set a warning for Windows users.
+  drush_environment_check_os();
+
   // Process the site alias that specifies which instance
   // of drush (local or remote) this command will operate on.
   // We must do this after we load our config files (so that