OK, I think I have it; in wp-content/plugins/autoptimize/classes/autoptimizeBase.php in the hide_iehacks-function on line 84 could you replace
'#<!--[if.*?[endif]-->#is',with
'#<!--\[if.*?\[endif\]-->#is',Could you see if that fixes the problem for you and confirm if so (or if not)?
Stupid bug really, don't know how I missed that ... :-/