This is because in the original nUI the Worldfram (gamescreen) has been moved up so you can still see everything, in InvisiSkin you don't need to do that, so by removing a line of code we can move the screen back to it's original position and thus lose the ugly black line.

To restore the Worldframe (remove the ugly back line):

1. Locate Interface>Addons>nUI>Main>nUI.lua
2. CREATE A BACKUP OF THIS FILE AND SAVE IT SOMEWHERE SAFE
3. Open the file
4. hit Ctrl F to bring up the find dialog and find 'WorldFrame', there is only one instance of it in this file
5. delete the whole line:
6. Code:
7. WorldFrame:SetPoint( "BOTTOM", nUI_Dashboard, "CENTER", 0, 0 );
8. save the file

You can edit this line whilst WOW is running if you wish, just make the edit, save the file and type /rl in wow to reload the UI.