Hi Pascal;
Did a quick test, adding this;
function my_scripts_method() {
wp_enqueue_script( 'scriptaculous' );
}
add_action( 'wp_enqueue_scripts', 'my_scripts_method' );
to the functions.php of my testblog and can't reproduce I'm afraid.
Although 1.9.3 featured a change in how Autoptimized hooked into wordpress (at init instead of template redirect, with another priority as well), this was reverted the next day in 1.9.4, so I would have no idea what would cause this behaviour (which would mean almost no scripts would be added to your page, as every plugin and theme is bound to use that function).
What I would propose in order to identify the reason for this erratic behavior;
* keep AO active and disable your other plugins (and maybe briefly swith to another theme as well)
* check you phperror-log for relevant information
* consider rolling back to AO 1.9.2 (download here) to see if this indeed would solve the problem
* if your code differs substantially from the one above (which I copy/pasted from the codex.wordpress.org), then post a (minimal) example here for me to test against.
Looking forward to cracking this little mystery! ;-)
Kind regards,
frank