I fixed this today...sort of. Although the archives still don't show up anywhere. But I got the Archive option back by going into Build Settings for the project and re-assigning my certs under "Code Signing Identity" for each build. They seemed to have gotten reset to something else when imported my 3.X project to 4.
I also used the instructions found here:
But I still can't get the actual archives to show up in Organizer (even though the files exist)