I'm having the same issue. When activated, my site loads fine in Chrome and IE explorers, but the stylesheet for the theme is missing in Firefox and other third-party browsers.
I deactivated the plugin and my style sheet shows up. I tried manual minify and tried adjusting setting and nothing works. Seemed to work fine with the prior version of W3TC, but this newest update is what is causing the problems.
Anyone know how to fix this? Is there a setting that is triggering this problem?
I'll probably de-activate the plugin so I can keep my style sheet until I figure out what is causing the bug. Please check out browsershots to see what I mean - you'll see some pics look great, and some have the stylesheet gone: http://browsershots.org/http://www.sharpefit.com/order-shakeology/
Site is: http://www.sharpefit.com