Good news:
They are aware of it & the info has been passed to the devs. Here is a response from over a month ago: http://forum.square-enix.com/ffxiv/t...=1#post1219587
Originally Posted by Elrisivana
Thank you for posting your concerns about receiving duplicate Artifact Armor. I have made sure to submit all of your information to the development team, and they will thoroughly investigate this matter, based on your report. Unfortunately, I cannot guarantee that a direct response will be posted on this thread, but I do recommend checking Here or Here for any details regarding the development team's investigation. Thanks again for your report!
Bad news:
It has been a month since and it still isn't fixed. Until it is, always have your version 1 AF for the job you are doing with you, either in your bags or on your character when doing the new AF quests. You will still complete the quests, but you won't get duplicate AF since it can tell you have it with/on you.