Odds are you have two copies of WoW installed now... if you look in your file system you'll almost certainly find that there's a directory for [ C: > Users > Public > Games > World of Warcraft > Interface > AddOns ] and that is where you should be installing nUI.
The old [ C: > Program Files > World of Warcraft ] path does not work well in Windows Vista and Windows 7 because WoW can't write to that directory tree (permission issues) as part of the security settings of Windows.
I'm not sure I would suggest deleting what's in the program files directory though. Just look and see if the Users\Public path exists and try putting nUI in there and see what happens.
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