Currently the scripts aren't run with a specific siteaccess this means that the database information must be specified in thew override site.ini file.
This is something that we will look into for an upcoming release.
For now you can edit the runcronjobs.php script and add:
$access = changeAccess( array( 'name' => 'mysiteaccess', 1 ) ); where mysiteaccess is the name of the siteaccess you want to use, eg. user, admin or a custom one.
