Hi,
I upgraded w3 total cache on one of my client sites (sorry I'm not sure which version it was running before as I don't have a complete backup from then) and in the process the auto minify stopped working. As in, the files were being created fine on the server but something was causing a 500 internal server error when trying to access the files on the web.
I asked my hosting company and they told me to comment out the line on /wp-content/cache/minify/.htaccess:
Options -MultiViews
Once I did, the css and js were able to be accessed again, but I'm stil receiving the minify auto failure message in the admin backend when I first set the settings. If I click to another section then back to main the error disappears.