After some additional testing it appears that the first time after the cache is cleared W3TC is returning a zero byte gzip file for the minified CSS/JS. This is causing the browsers to throw the error I am seeing. After much hair pulling and head banging I ended up disabling minify within W3 Total Cache and using Better WordPress Minify instead to do the JS/CSS minification. it worked pretty much out of the box with very little configuration.
Frederick great work on W3TC, I know it is a lot of work to build and maintain such a complex and comprehensive plugin. If you would like more info to help debug the issue I was having I would be happy to discuss via private message or email.
