Custom save button shows ‘Are you sure you want to…’ dialog

SOLVED: Found the solution. Trick is to disable the autosave. But take care to only do this on a non-ajax save.

add_action( 'admin_enqueue_scripts', 'my_admin_enqueue_scripts' );
function my_admin_enqueue_scripts() {
       if ( defined( 'DOING_AUTOSAVE' ) && DOING_AUTOSAVE ) return false; // don't disable if it is an auto-autosave
    if ( 'POST_TYPE' == get_post_type() ){

       wp_dequeue_script( 'autosave' );    
    }
}

Hope this helps someone.