I've been using two-factor authentication successfully for a few weeks.
Today I installed the Google Analytics plugin by Joost. As soon as I went to save the settings for that plugin, I was asked to log in, I tried, and was told that the code (from Google Authenticator) was wrong (I checked carefully that I typed it correctly, no shift-lock or anything).
The new plug in may or may not have anything to do with this issue, as I have never had to log in with Two Factor auth before (I've stayed logged in).
I don't know what more to offer, but let me know what you might need to identify a potential conflict or resolve this.
PHP 5.4, WordPress 3.5.1