I am supporting someone whose EndNote X7 plugin for Word 2013 won’t retain the setting to load it when starting Word. If you manually enable it, it works and stays on, but if you exit Word and then relaunch, it’s back off again. i.e. it will not stay on/load persistently and automatically, only manually.
I was able to resolve this by editing the registry entry in her HKEY local users for the EndNote add-in entry. Changed the value from 0 to 3 to force the add-in to load every time. Tested this through several relaunches and the add-in loaded each time.