At file script-loader.php the following line can be found:
$scripts->add( 'scriptaculous-root', '/wp-includes/js/scriptaculous/scriptaculous.js', array('prototype'), '1.8.0');
It defines the Scriptaculous-root file to original one. If you only want to load effects.js you would address this using:
wp_enqueue_script('scriptaculous-effects');
But it behaves not as expected, it loads nevertheless all components like slider.js, builder.js and so on too.
Solution:
The definition of scriptaculous-root is wrong and should address the right file instead:
$scripts->add( 'scriptaculous-root', '/wp-includes/js/scriptaculous/wp-scriptaculous.js', array('prototype'), '1.8.0');
in other words it should be .../wp-scriptaculous.js instead of .../scriptaculous.js because the original file loads by default all components and the wp- version doesn't load them (opposite behavoir introduction by mdawaffe serveral versions ago).
