Not quite finished with updates to 5.8 and 5.9 is released fixing a security vulnerability thought to have been fixed in 5.8.
I wouldn't try this with a 5.x to 6.x upgrade but
- untar drupal-5.9.tar.gz
- mv sites/default/settings.php settings.php.org
- cp -a drupal-5.9/* drupal_core_directory
I did have css cache problems afterwards but disabling and re-enabling caching cleared them. drush cache clear works better.
Permissions can be an issue too. files/css on an ubercart installation was set to 775. Changing owner and setting to 777 cleared errors.