Did you by any chance change resolution? I briefly went to 1024x768 and lost the minimap, but when I went back up, it was back. Note: I did not try again to confirm that was the reason I lost the minimap.
Definitely some bugs to work out. Yesterday I was standing outside the Bearded Rock crystal and it and all the mobs were gone, while people kept coming from Limsa and asking if they were in the right place.
I said that "It's been gone for an hour and we're waiting for it to be respawn" and I felt guilty because someone believed me and got angry and logged off before I or anyone else could correct me.