The 'Automatic URL alias' checkbox state is now stored in the database

The functionality offered by the Pathauto Persistent State module has been merged into the Pathauto module. Previously, the module attempted to auto-calculate the state of the checkbox seeing if the current alias matches what the automatic alias would be for the entity (detailed in https://www.drupal.org/node/1167612#on-demand).

Previously, if you saved a node using node_save() (and not through the UI), then it may have caused any content that had a manual alias (the "Automatic URL alias" checkbox being unchecked), to suddenly have an automatic alias generated for it. This is an unwanted behavior that was experienced when using moderation modules.

If you already had the Pathauto Persistent State module enabled, then when you run update.php (or drush updatedb), the existing data in the pathauto_persist table will be copied to the new pathauto_state table, and the module will be automatically disabled for you. You should feel free to uninstall the Pathauto Persistent State module at that point manually.