Ok, so further testing indicates that it only happens on users that were created in 0.6.1(via an import from SMF) and new users work fine. I can fix it by blanking out the user's email and then putting back in the correct email.
(For clarification this is running on a pull from the 0.7.0 dev branch from yesterday)
That warning means that someone is running a very old version of NodeBB's client side code (and simply hasn't refreshed, or hasn't cleared their browser cache). So not to worry 🙂