I have never used an automatic upgrade for plugins or WP. Normally the way I do it is to deactivate the old plugin. Then rename the old plugin directory by adding the version after the directory name. Then I unzip the plugin files and manually install them into the wp-content directory.
I think for W3TC I also manually removed the cache directories, so that there would be no old cache files lurking around.
Then I activated the W3TC plugin and configured it. Once I got the correct mod_rewrite installed in the virtual host, minimize worked correctly and enhanced page cache also worked correctly on all of the installations. A couple were upgrades from an older W3TC and one was a Super Cache. Once everything works correctly I remove the old directory from the server.
If you don't feel comfortable trying that method, then just use the older version until the next W3TC comes out. You should also have a backup before you modify the site.
Craig