I had the same issues on most, but not all, of the build configurations (Vista Debug Win32 came out correctly for some reason). Here's how I worked around it/solved it:
Opened the nnn_package.vcxproj file in another editor.
Noticed that the entry for the above build configuration (vista|debug|win32) was located by itself, separated from all the other configuration entries by a "PropertyGroup" entry that, amongst other things, set "PackageDir"$(OutDir)nnn_package"/PackageDir"
(replace the " with less-than/more-than)
Moved this section to -after- all the build configuration entries and saved.
Reopened solution in VS2012 and now all packages output to the correct folder regardless of configuration name and platform.
Hope this helps.