One workaround to consider trying would be to try binding a different key combination and see if that works.
Is there anything potentially unique or different about your location or keyboard configuration? As I commented before, there are some known bugs in Electron (the framework on which Evernote desktop is built) which could be impacting the Cmd-` functionality.
IS ANYONE FROM EVERNOTE EVEN READING THROUGH THESE THINGS!!?! This is even worse than that removing the multiple TAB option.
