I was a bit puzzled at first because I have never seen that before, and the upgrade process is dramatically slower this way.

After googling, I realized that all the WP files are now owned by my webroot account and apache no longer has exclusive access to them.

the simple fix was to give apache ownership of the WordPress directory.

#: chown -R   apache-user: wordpressRoot

This does pose a potential security risk. However, this already exists on every WP site that has auto upgrade working. Most shared hosts will run the apache instance under your username so you don’t see this problem.

If you are concerned about security, I would suggest you leave the permissions as they are… or use Drupal. =p