In addition to the applications that are in the startup folder, there is another place that contains startup applications. These items are stored in the registry in the My Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run key. This is a good place to start looking when you can’t figure out where some spyware or other application is being launched from.
When you look in this key, anything that is being launched from My Documents is probably wrong.