Bit of an odd one, this.
Evernote keeps opening when I start up my Mac and login. I don't want it to. Happy for Evernote helper to sit in the background, but I don't want the program to open.
I've turned off 'Open in Login' on the Dock item. I've done the Preferences -> Users and Groups -> Login item and only the Helper is listed there. I'm quitting the program when it opens, not just closing its windows, so it shouldn't be a 'Reopen windows when logging back in' function of OSX.
I barely use Endnote, because at one point it made it really annoying to access notebooks in t