Well, this is the way W3TC + AO (should) work;
1. page is requested
2. W3TC checks if the page is in cache (HTML including references to Autoptimized CSS & JS) and if so sends that as response to the browser
3. if not in cache, WordPress creates the HTML
4. AO receives the HTML, aggregates the CSS & JS and checks if it has a minified version in cache of exactly the same code (to the last comma) and if so replaces all original CSS/ JS with links to the optimized CSS/ JS in cache
5. if not in cache, the CSS/ JS is minified, cached and replaces all original CSS/ JS with links to the optimized CSS/ JS in cache
6. AO returns HTML to wordpress
7. W3TC caches HTML
7. HTML is sent as reponse to the browser
So if your CSS/ JS are recreated time and time again, there are 2 things happening;
1. W3TC is not able to cache pages (else AO is not even called; the HTML has links straight to the cached CSS/JS)
2. AO does see differences in the code (however small).
Do you have a URL where I could have a look to find confirmation of these “theories”? 😉
frank