hook_form_aaaaarrrgh-alter!! Please help before I jump out of the window in despair

I'm trying to upgrade the checkout module to 4.7 and everything going tickety-boo... I've pretty much got the stuff about hook_nodeapi and hoo_form_alter sorted... BUT!!!

In my hook_form_alter I call drupal_set_message to warn the user that his node has been checked out when he loads the form to edit the node. When I press on "Submit" the node is updated... and the message still gets displayed, just above the "page was updated" message. What is happening? Is hook_form_alter getting called twice? Has the message not been cleared, and if so how to clear it?

Here is the code:

function checkout_form_alter($form_id, &$form) {
  global $user;
  if (isset($form['type']) && $form['type']['#value'] .'_node_form' == $form_id) {
    if (user_access('checkout documents')) {
      $node = $form['#node'];
      if ($node->nid) {
      	$data = checkout_checkout($node->nid);
        if ($data->uid != $user->uid) {
	  checkout_message($data);
	  }
	if (variable_get("checkout_long", 0 ) > 0) {
// _form_form code follows:
	  $form['checkout']['checkout'] = array(
	    '#type' => 'checkbox',
	    '#title' => t('Checkout this document on saving?'),
	    '#return_value' => 1,
	    '#weight' => -15,
	    '#default_value' => FALSE,
	    '#description' => t('If you want to check out this document and so prevent other users from modifying until you next edit it, then tick this box'),
	    );
// the final return is not needed because $form is a reference.
           drupal_set_message(t('This document is now locked against simultaneous editing.  It will unlock when you navigate elsewhere, unless you check the box to reserve the document in your name.'));
  	  }
	else {
          drupal_set_message(t('This document is now locked against simultaneous editing.  It will unlock when you navigate elsewhere.'));
          }
        }
      }
  }
}