W3TC no longer handles minification of our JS and CSS files correctly.
The files get minified as before, but do not get removed from the page output!
So consequently our site's pages have major duplication - the original JS/CSS files still remain in there, plus now they also have the minified versions included as well... Not helpful.
It worked perfectly before upgrading from the old 0.9.2.4 W3TC version (using Manual configuration), so something new has been introduced since then to make minify no longer work properly.
We had to disable W3TC's minify function and add/use the separate WP-Minify plugin instead to get our site output working right again.
For more, see this thread: