After updating to version 0.9.4 on my dev system (with WP_DEBUG on), I always get a PHP Notice - on every site (and I have deactivated W3TC!)...
Notice: Cannot find configuration key extensions.settings. in .../wp-content/plugins/w3-total-cache/lib/W3/UI/Settings/SettingsHandler.php on line 91
It's just a notice, but maybe you can fix that in a later version.