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I am guessing that would be a change that blizzard introduced. The only thing nUI does with the minimap is place it in the center of the dashboard or let blizzard position it in the top right. Display of icons in the minimap itself would be something outside of nUIs control.
Have you tried it without nUI installed and see if you get the same problem. Some quest based addons or tracker addons may change the minimap icons so worth checking those out if you have them.
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