Upgrading this site from Drupal 5 to Drupal 6 has proven to be difficult - as the upgrade script encounters a infinite loop. And a bit of digging may have come up with part of the reason for this.
I had to manually skip the schema number 6021 upgrade of the system module - as the update process went into the infinite loop at this stage.
Doing this is a bit dangerous - as I had to kill off the upgrade process after it had run for 12 hours (!) - and then restarted, but I then manually had to increase the base version for the system module with 1 - and then it ran to completion
I now see other problems - so I will have to try to rectify these now.