I am getting Drupal messages stuck permanently in session, so that after being displayed they are not cleared. The unsetting code in function drupal_get_messages in bootstrap.inc is firing - It's as if the session is sleeping (i.e. serializing to disk) before the messages array is cleared.

Have you witnessed such a thing?

UPDATE The call that commits the session starts from drupal_page_footer at the bottom of index.php - for some reason this is executing twice per request! once with the emptied messages and then again with the messages back in the array.