Is the back up codes list time limited? I have mine saved in an email to myself, yesterday I was too lazy to turn my phone on to use the authenticator so tried using a code but none of them worked (I think I'd only used three up to that point) after a while got the 'too many log in attempts' message.
Finally turned the phone on and logged in with the authenticator, the list only had a line through three codes but I generated a new list anyway.
Not sure if it was a bug or me being an idiot somehow, but I'd used them before with no issue.