The plugin is a custom post type (
client_reference by default) and creates two menu groups - "Articles" (created automatically by WordPress for custom post types) and "Knowledgebase", which is where the "Articles" are displayed. Think of the articles as a custom post type designed to only be used in the WordPress administration panel.
As for replacing the Users menu, it looks like my plugin (stupidly) used menu position 70, which caused it to replace the Users menu (see http://codex.wordpress.org/Function_Reference/add_menu_page for default positions). I'll get a fix out for this today (you can track it here: https://github.com/stevegrunwell/wp-client-reference/issues/2) but it won't impact already-installed versions. To restore the Users menu, go to the "Options" page under "Articles" and change the "Menu Position" option to something besides 70 (new default will be 71).
I apologize for any confusion I may have caused you.