I have exactly the same issue. It's not all of my notes but just two of the notes I added recently. On the Mac app I see the notes fine and I also see them fine using a web browser.
I am also afflicted with the web clipper log out issue. My browser console is filled with these notices. Is this expected? a — port.js:155XMLHttpRequest cannot load safari-extension://com.evernote.safari.clipper-Q79WDW8YH9/1a0071f0/_locales/en_us/messages.json. Cross origin requests are only supported for HTTP.