Sooo this is a little odd but I've verified it on multiple networks.
I installed the Simple Social Icons plugin on my WP multisite and network activated it.
When I did this, the following plugins were "de-activated" across the network:
Akismet - http://wordpress.org/extend/plugins/akismet/
AddToAny - http://wordpress.org/extend/plugins/add-to-any/
Multisite Analytics - http://premium.wpmudev.org/project/google-analytics-for-wordpress-mu-sitewide-and-single-blog-solution/
The solution seems to be simply clicking "network activate" again on each of the 3 plugins, fingers crossed... (they are reactivated but no longer show as network activated?)
But this definitely seems to be a pretty big issue.
Has this plugin been tested on multisite?