I'm seeing this also. Very frustrating. Tried reinstalling from EN website. Using El Capitan GM and Evernote 6.1.1. On startup, it appears to render the window and then spins (displaying the beachball). Evernote (not responding). Need to force quit to exit.
I'm having problems with the Web Clipper on Safari and Mavericks. Specifically, most of the content links on sites like new.google.com are un-clickable. The only workaround is for me to uninstall the Web Clipper extension.