Display messages in bootstrap file
To get the list of the messages set with drupal_set_message(), you should call drupal_get_messages().

Drupal doesn't use any global $messages to store those messages. They are stored in $_SESSION['messages'], but you should really use drupal_get_messages().

drupal_get_messages() returns an array; this means you cannot simply use the following code.

$messages = drupal_get_messages();
print $messages;