I'm using W3 Total Cache with Amazon S3 as my CDN.
Let's call my website http://www.mywebsite.com.
When I have the CDN enabled, the CNAME for the assets becomes cdn.mywebsite.com.
This is great, but it seems that when using W3 Total Cache with the CDN option enabled, the media query strings that are appended after the static files do not appear. This is problematic because if I were to update a CSS file for example, the changes won't be reflected.
When my site has the CDN disabled, the media query strings do appear.
I believe there may be an issue with W3TC not recognizing the CDN URLs when rebuiling the page cache and appending the query strings to them. I didn't have this problem with an older version of the plugin, but I also wasn't using S3 for my CDN at the time.