I have a Premium account and just set up 2-factor authentication on my Evernote account. When the site displayed the QR code, I scanned it using the 1password browser extension and it auto-entered the produced code successfully. I then went to test the 2-factor auth by signing out of the Evernote website and signing back in. I entered my password successfully. Then when the site asked for the 2-factor auth code, "Enter the code displayed in your Google authenticator app," 1passworded auto-filled the code. When I pressed "Sign in" this message appeared "The code you entered is not valid" and I had to request a text code to complete login.
I see the Evernote 2-factor auth setup site says, "Set up a preferred authenticator app (optional for paid subscribers)," and a premium account is a paid account, so I hope that's not the issue.