New custom post type entries are not sorted correctly in admin using pre_get_posts

Question

I am working on a WordPress plugin and trying to use the pre_get_posts hook. Everything seems to sort, but when I add new items through the back-end, they get added to the bottom and not sorted for some reason. Hoping a fresh set of eyes could help.

add_action( 'pre_get_posts', 'simple_class_custom_query' );

function simple_class_custom_query ( $query ) {
    // Sort Archive Page Results
    if ( is_post_type_archive( 'simple_class' ) && $query->is_main_query() ) {

        // Sort results by class day
        $query->set( 'meta_key', 'class-day' );

        // orderby class start
        $query->set( 'orderby', array( 'meta_value' => 'ASC', 'class-start' => 'ASC' ) );

        // Hide hidden classes
        $query->set( 'meta_query', array(
            array(
                'key' => 'hide-class',
                'value' => '1',
                'compare' => 'NOT EXISTS'
            )
        ));
    }
}

Thanks in advance! Should add this has a few pieces. The hide-class is a meta checkbox to hide the class and the classes should be sorted by the day of the week the class takes place and then by start time.