This problem is now fixed. For anyone else having the same problem, the problem was that the new 3.0 capabilities, edit_theme_options weren’t added. This code fixed the issue:
$role =& get_role( ‘administrator’ );
if ( !empty( $role ) ) {
$role->add_cap( ‘update_core’ );
$role->add_cap( ‘list_users’ );
$role->add_cap( ‘remove_users’ );
$role->add_cap( ‘add_users’ );
$role->add_cap( ‘promote_users’ );
$role->add_cap( ‘edit_theme_options’ );
$role->add_cap( ‘delete_themes’ );
$role->add_cap( ‘export’ );
}