I have w3tc configured with page cache, minify, object cache, db cache, browser cache, CDN.
Have you had the same problem?
In the Minify settings I have V checked:
Rewrite URL structure
Automatically upload modified files
HTML minify settings: Enable
JS minify settings: Enable
CSS minify settings: Enable
WordPress 2.9.2 and W3TC development version circa 20/06/2010.
edit: tested under Firefox 3.6.3 and Chromium 6.0