I'm using W3 Total Cache 0.9.0 with WP 3.0 and Thesis 18b1.
Here's what I do:
1) Make a change to custom.css
2) Re-upload the minified CSS to CloudFront through W3 Total Cache
3) Dump all the caches through W3 Total Cache
4) Dump my local browser cache
5) Load the page
The change I make to the CSS file does not show up. If I disable W3 Total Cache, the change does show up which is why I think it's the plugin and not WP or the theme that's causing the issue.