I opened a ticket and support directed me to uninstall then reinstall Evernote completely.
Short answer, that worked for me. I have full function of screen, window, and selection capture, and regardless of which Mac desktop I initiate from.
Long answer: I was using the Mac App Store version, and after uninstalling and the reinstalling that version, the issue persisted. Then I uninstalled but reinstalled with the standalone version, and everything works properly.