Membership2 Kills all plugins after update and reactivation

Every time Membership 2 Pro updates it kills all my plugins and plugin settings upon reactivation.

This is a horrible response for my business. This means if my members are doing anything on my site everything dies until I go through each plugin and turn each one back on and reset everything.

Even the Membership Protected Pages all reset and Protected Menus Reset and adds System Subscription to list of subscriptions with (even though I delete it every time).

Can someone please fix this. I am sure there will be plenty more updates but this will cause some very horrible business downtime and cause us to loose affiliates if our site goes down every time we update a plugin.