hi scott;
that's a known issue with plugins that inject page- (or request-)specific JS (or CSS) into the HTML (cfr. the FAQ) which breaks all caching.
As a solution you can hunt down the "ever-changing" JS or you could disable the aggregation of all inline JS using the API ("autoptimize_js_include_inline"-filter) as shown in autoptimize_helper.php_example.
hope this helps,
frank