When you fill the Excerpt box with any text on post edit page, the_excerpt() function doesn't add any read more or ... at the end of the short description. Read more is only included if Excerpt is set empty, and this is not a bug, it's a feature.
Now the solution is to avoid the excerpt_more filter to return read more, and use the the_excerpt hook. But excerpt_more should be set the empty to make sure double read more is not displayed. So, the code you need
function new_excerpt_more($more) {
return '';
}
add_filter('excerpt_more', 'new_excerpt_more', 21 );
function the_excerpt_more_link( $excerpt ){
$post = get_post();
$excerpt .= '... <a href="'. get_permalink($post->ID) . '">continue reading</a>.';
return $excerpt;
}
add_filter( 'the_excerpt', 'the_excerpt_more_link', 21 );