WPMU Plugin Manager Bugs

Not sure what category to post this in since it's not premium..... but wanted to give dev and other users a heads up.

We've had random plugins being turned off across out install and couldn't figure out how this could be happening since our users don't have access to plugins.... the most prominent plugin we've seen the issue with on a consistent basis is AllInOne SEO but we've had the issue with other plugins as well.....

It turns out that we are able to reproduce the issue by using the WPMU plugin manager, if we deactivate any plugin sitewide via the Plugin Manager, AllInOne SEO will consistently be turned off as well on every site on the install, even if it is never specifically touched via the WPMU Plugin manager.

Deactivating a plugin intentionally sitewide via the Plugin Manager can also cause other plugins to turn off as well although it isn't always across every site on the install like it is with AllInOne SEO. For example, the issue occurred last night when we mass deactivated a plugin sitewide and another random plugin was also mass deactivated but only on limited random sites.... weird.... but this did break the sites since the plugin's code was inserted via shortcode.... making this issue dangerous to say the least.....

In any case, I suspect others may have the other problem of random plugins mass deactivating but can't put their finger on the cause, it took us a long time to figure out the association.... if so, hope this helps!