Pro Sites premium plugins self-activating on mainsite

I don't know if this is a Pro Sites issue, but I have posted it in Plugin Support.

On our mainsite, a message is displayed at the top saying: "There are pending changes to your account. This message will disappear once these pending changes are completed."

I don't know where this is coming from? The major problem is, that we have a lot of plugins for our eating users, that is auto-activating on their site, when they upgrade, but it seems like the plugins are auto-activating on the mainsite too, even though this isn't a Pro blog.

You have support access to the site. Please help