I have been banging my head against the wall for days, trying to figure out why some of my startup items are duplicated. Apparently, when I first installed Windows 7, I was trying (unsuccessfully, I might add) to organize my start menu, I copied files from the All Users start menu folder into my start menu folder. Windows updated the Registry, pointing the Common folders to my user folders. Hence, when Windows checked for startup items, it found the shortcuts in both the Common user folder as well as my user folder (being the same folder twice).
It was weird, when I looked in the startup folder, there was only one copy of each shortcut. When looking in MSCONFIG, each item was duplicated.
Below is a post I found that helped me fix the issue.
http://www.sevenforums.com/general-discussion/24569-startup-folder-2.html#post510414