The plugin says it is compatible with version 3.0, but uses functions that are deprecated for WordPress 3+ - get_usermeta and update_usermeta.
Also note that it adds tons of options to wp_options, but does no clean up on uninstall. You need to manually delete the options. This is a shame, b/c both the deprecated code and creating a clean uninstall would be very easy to fix.
However, the worst part was that it creates errors in WP, b/c it apparently incorrectly writes some data to wp_usermeta, which then creates problems in wp-includes/functions with get_all_user_settings(). The problem continues even after removing the plugin and all entries it created in wp_options. Run the plugin (on a backup, offline copy of a site) with define('WP_DEBUG', true); in wp-config.php and you will see all the errors it throws (dozens for each user in your database when you clone, several on every admin page in your site even after you've removed the plugin and manually cleaned up all the options it leaves behind).
I deactivated all plugins, replaced all core code with fresh copies, etc. before I finally tracked it down. I had to delete a bunch of settings in wp_usermeta, which this plugin had changed when it 'cloned' settings for a user. Once I removed those settings, the site was back to normal (so!!! glad it was an off-line test site).