The add_action priority change from 2 to 11 on the following Line 308 in autoptimize.php in AO Versions 1.9.0 and 1.9.1 disabled all optimization on thousands of, but not all, pages at a large website am developing offline.
add_action('template_redirect','autoptimize_start_buffering',11);
I haven't determined the reason yet, but wanted to let anyone who may have that problem know that reverting from Priority 11 back to 2 corrected it at my development site.
That site uses WordPress 4.0, Ubuntu 14.04.1, Apache 2.4.7, and PHP 5.5.9, although the priority issue more likely is due to the relative processing priority of other plugin code than to any of that.