Having a problem that I'm sure you'll be much quicker to fix than me! My Buddypress installations on separate networks are sharing content...ie, activity on one is reflected on the other.
I started fresh with a new install and it's still happening, so I'm guessing I've misunderstood a step along the way.
1. Install latest WordPress.
2. Enabled Multisite in wpconfig and activated through the dashboard.
3. Uploaded WP Multi Networks to my plugins folder and activated.
4. Created an mu-plugins folder in wp-content, uploaded the BP Multi Network plugin to it.
5. Created two subnetworks.
6. Added Buddypress to each and activated.