Same problem here! ArenaNet seems to be already aware of the problem and is investigating.
I use the Google Authenticator App not just for GW2 but for other websites and services as well. And for those, other services, the app works fine. So really just a problem for this game.
I wouldnt want to switch to SMS authentication since (a) cellphone numbers can get hijacked here pretty easily, and (b) sms messages here can get delayed at times so it can be more frustrating. I can bear the inconvenience for now, but I hope ANet gets a fix in soon!