I develop a plugin with custom fields.
Look at
wp-admin/user-new.php
Line 76
wpmu_signup_user( $new_user_login, $_REQUEST[ 'email' ], array( 'add_to_blog' => $wpdb->blogid, 'new_role' => $_REQUEST[ 'role' ] ) );
I think it should be
wpmu_signup_user( $new_user_login, $_REQUEST[ 'email' ], apply_filters("add_signup_meta", array( 'add_to_blog' => $wpdb->blogid, 'new_role' => $_REQUEST[ 'role' ] )) );