Agreda,
I’m running WordPress 3.0 as a network, and ran into a similar problem. Whenever we create a new site, it wants to use the Twenty Ten theme, even though it’s disabled for network use. So after a little searching, this is what I located. Inside the wp-includes folder is a file named default-constants.php. On line 293, you’ll find the following line:
` if ( !defined(‘WP_DEFAULT_THEME’) )
define( ‘WP_DEFAULT_THEME’, ‘twentyten’ );
}’
So basically, that’s defining the folder twentyten as the default directory. You can set that to a different theme directory to change the default theme. This should initialize on a fresh install, but you might have to change the database entry manually on a site that’s already created.