It sounds like (a) you have another addon that is "breaking" nUI when you log in since the patch -- probably one of the addons nUI integrates like Recount, Omen3, Skada, Titan Panel, FuBar, Chatter and/or Prat. It could also be Grid, Healbot or one of the other addons supported by nUI Info Panel plugins... so make sure those are all current.
As for the animations turning back on when you close the map... there's something odd going on there. It sounds like something is causing you entire UI to be reloaded when the map closes and that's not right.
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