I tend to have 5-6 instances of Finder open so I can easily navigate to various files I use regularly. (See http://forums.macrumors.com/threads/need-better-workflow-to-organize-my-files.1981374/) I just upgraded to El Capitan, and whenever I shut down - usually once a week - when I start back up, all of my Finder instances are closed. Why is that? On my first Mac which ran Leopard/Snow Leopard/Mountain Lion I never had this issue. It is annoying and a pain to have to open everything back up again.