This is not a question but a bug report of the WPMU Dashboard not playing well with Bulletproof Security and Wordfence plugins. Maybe other plugins as well. I notices now on several of my sites when updating Bulletproff Security, or, after recently installing Wordfence, the WPMU dashboard menu item disappears from the WP dashboard. All it takes is to go to the plugins page and deactivate WPMU dashboard and reactivate it again. The menu then reappears.
However, when this happened the first time it was a bit of a scramble to figure this out. I realized that having WPMU plugin updates dependent on having WPMU dashboard installed is a major pita. I think it should be an option and not a requirement.