I’m having this problem also.
WordPress version: 4.5.3 (WP Engine)
PHP version: 5.5.9-1ubuntu4.17
Network-installed plugins (all are network-activated):
* BuddyPress 2.6.1.1
* Google Analytics+ 3.1.5.1
* Multisite Enhancements 1.3.5
* Multisite Plugin Manager 3.1.4
* Multisite Theme Manager 1.1.3
* WPMU Dev Dashboard 4.1.1
plus BuddyPress Default Data 1.1 (network-activated).
My Network Admin “Tools” menu only has:
* Available Tools
* Buddypress
(and the Available Tools page does not show anything for BuddyPress Default Data).
When I look in the primary BuddyPress network site (using default BuddyPress config, no changes to wp-config.php), I can see that the BuddyPress Default Data plugin is network-activated, but I also don’t have anything in the Tools menu that shows BuddyPress Default Data (just Available Tools, Import and Export).
Hope you are able to resolve this soon!
Cheers,
AB