Lately, when bring up a new site, I have had a problem with Drupal creating user 1 correctly or at all.
What I have been doing is manually updating the user table with name and temporary password hash.
To do this I have been using MySQL Buddy. It's a slick web interface to interact directly with databases on the MySQL server. But at some point I'll just use a CLI update command.
This is occurring on a multi-site installation of Drupal 6.