After the plugin is installed it starts to generate cache files in the wp-content/w3tc directory.
Then if the plugin is set to cache files in memcached the disk cache is still hit until all the files, or files and directories, are deleted in wp-content/w3tc. Perhaps the cache could be emptied automatically when a new cache setting is chosen.
Sometimes the cache is not cleared completely when empty cache is clicked, so it is necessary to restart, or stop and start, of the memcached demon is necessary. Could you add a button that would kill -9 memcached-pid, then restart memcached using an init script if one is installed. To make this accurate the location of the init script could be set in the settings, or an init script could be generated by the plugin by filling out a form with the choices needed for a good startup, such as:
/usr/local/bin/memcached -m 512 -c 512 -t 4 -l 127.0.0.1 -p 11211 -d -u memcached