This is more informational than anything, and I'm not 100% sure what happened.
Last week I did a php update and update to latest version of Apache. About the same time, the changes may have not been related, one of my Multisite sites started acting strange. Dropped out of Google Analytics, stopped redirecting, caching stopped working, etc...
Somehow, Plugin Organizer disabled many of the plugins that should have been active for the site. Took me a while to figure it out and re-enable what I needed.
Again, I'm not sure why or how this happened. I will be happy to answer any questions or do what I can to help you improve the plugin. Beyond that I just wanted to let you know it happened.