Foglight is part of the default Cart install. It allows you to see all of the map even if you haven't explored it yet.
The map on the rightmost side of nUI sometimes shows the full map at other times it shows the map like nothing has been discovered, even if you have discovered areas.
The map in the lower right of nUI is the Zone Map. It looks as if you aren't the only one that is happening to. A couple of other Cartographer users have reported it, both here and on Curse.com. It's also shown as a bug ticket through the reporting feature on Curse. So at the moment, it's a known bug between Foglight and the Zone Map (the little one you can get from hitting shift-m).