There is no such thing as "Documents and Settings" folder in Windows Vista or Windows 7: what you are seeing is only there to trick bad programs into thinking it's there. It just re-points to the users directory. Programs that were hard-coded to only point to the Documents and Settings folder are fooled by this repointing so they don't crash.
It's not an issue with your computer, and you're highly recommended to simply hide protected operating system files in your folder options so that you don't mistakenly think there are duplicates or try to modify this link.
In addition: you are referring to Documents vs. MyDocuments. The one with the word "My" is a folder, while the other is simply a library that is told to display the contents from several locations, including the "My" folder. Think of a library as an instant search: every time you open it, it searches the "my" folder (and any other folders set for that library) and displays everything it finds.
In short: there is no actual duplication, it's all in your mind :)