The PathAuto issue about manual aliases being automatically replaced is currently closed for additional comments, awaiting the results of a chipin for further development. I post a newbie's cumbersome workaround here in case it helps others like myself who only have this problem with a couple of nodes.

For the content-type involved, make sure it uses the title of the node as the alias (in Automated alias settings). Then, when you're editing the node, just use the alias you want as the title. To modify the title itself, add the following to your template.php file:

<?php
function metramomes_preprocess_node(&$vars, $hook) {
  if ($node->type == 'your_content_type' && $node->title == 'your_node_title') {
    drupal_set_title('The Title You Want Displayed');
  }
}
?>

It's a quick and dirty solution until PathAuto is updated. Don't bother with this if you have 500 nodes to take care of...