Lion not recongizing main folders after Migration Assistant

[Espilon38]

I have a bit of a problem, I recently bought a new MacBook Pro, and I love it. I have all my stuff from my old Mac stored on a Time Machine backup. So I went into Migration Assistant and transferred all my data from the backup to the new computer. Everything transferred over fine, but now all the folders inside my home folder, including the home folder, seems a bit confused. The folder icons don't have their special imposed image on the folder like they usually for music, pictures, movies, downloads, etc. The desktop folder is the same way, what ever I have in the desktop folder isn't actually in the desktop folder. It's as if the computer isn't recognizing them as those kinds of folders. I'm afraid it's like this because when I first booted up the computer, I made my account settings they same as they were on my old Mac. When it came time to transfer, I had to make another dummy account so that the current one could be replaced with the backup, since they had the same username. Should I have not made it replace or is just how Lion did files and how Snow Leopard did them? Any help would be appreciated. Also, it will not let me select those folder (movies, pics, etc.) as favorites.