I'm using W3TC 0.9.1.3, WP 3.1 and Cloudfront and I *think* I have a similar problem.
I have "Host minified CSS and JS files" checked, I definitely hit the button to upload these files, I see them in my S3 bucket, but no dice, even after emptying all caches, my page still refers to the combined CSS file on my local disk, not the CDN:
<link rel="stylesheet" type="text/css" href="http://iko.wp_bm/wp-content/w3tc/min/b7912a/default.include.548125880.css" media="all" />
yet it was definitely uploaded by W3TC to the CDN:
or via my CNAME pointing on Cloudfront:
Some other elements on that same page are using my CDN correction, for example: