I am running Drupal 6 and have attempted to update the Core about 5 times recently, and it continues to tell me I haven't updated it. I AM running update.php, and doing it the way it's always worked before. But Drupal is not perceiving that I've done it.
No problems with individual modules updates. Drupal and following a procedure I've followed numerous times before, successfully. Not using Drush, but am using command line.