Upgrader Issues

New install of WP on the server, that I upgraded to 2.8.4. I notice that I’m being prompted to upgrade some plugins, so I select the “upgrade automatically” feature.

System seems to just hang.

Error messages are as follows:
Aug 27 20:21:27 excitebike pure-ftpd: (saas@127.0.0.1) [NOTICE] Deleted /public_html/wp-content/upgrade/core/wordpress/wp-includes/post.php
Aug 27 20:21:27 excitebike pure-ftpd: (saas@127.0.0.1) [INFO] Can’t change directory to /public_html/wp-content/upgrade/core/wordpress/wp-includes/query.php/: Not a directory
Aug 27 20:21:28 excitebike pure-ftpd: (saas@127.0.0.1) [NOTICE] Deleted /public_html/wp-content/upgrade/core/wordpress/wp-includes/query.php
Aug 27 20:21:28 excitebike pure-ftpd: (saas@127.0.0.1) [INFO] Can’t change directory to /public_html/wp-content/upgrade/core/wordpress/wp-includes/registration-functions.php/: Not a directory

The updater seems to be updating to directories that don’t exist.

Any advice on how to resolve? Do I need to do a clean install of WP to resolve this?