El Capitan Server Not Disconnecting Users

I am running a file server on El Capitan and it would not automatically disconnect users when they log off from client iMacs (running Mavericks). At the end of the day there are more "connected users" than the actual number of connected users. When it's time for the server to restart itself (3:30 AM), it would not do so but instead shows a prompt windows "There are XX users connected, blah blah blah" when in fact there is none. It's almost exactly like this problem except the different OS version and it had no solution either: Mavericks Server Not Disconnecting Users

I want the restart feature to work on its own. How do I get it fixed?