I had a problem with a program shortcut in my Startup folder that would launch with an error that the program was already loaded. I figured out that not only was the shortcut in the Startup folder for "All Users" but that my user account Startup folder was also considered to be that same "All Users" folder (%ALLUSERSPROFILE%\Start Menu\Programs\Startup) [I'm using the universal direction here. You can type %ALLUSERSPROFILE% and %USERPROFILE% into the Run box in the Start Menu to find the specific absolute paths for your system]. In effect, everything in the Startup folder would launch twice: once for "All Users" and again just for my account, even though it was the same folder.
To fix this, I created new folders: %USERPROFILE%\Start Menu\Programs and %USERPROFILE%\Start Menu\Programs\Startup which were missing. I then used RegEdit to go to the registry key HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders and made sure the values Start Menu, Programs, and Startup pointed to the folders in my user account folder and not the All Users folder. Now, my Common Startup and user Startup folders were different.
Related: in Regedit, use String values [REG_SZ] for absolute paths (e.g.: C:\Documents and Settings\Administrator) and Expandable String values [REG_EXPAND_SZ] for the %-style paths (e.g. %USERPROFILE%).
Reference: http://windowsxp.mvps.org/usershellfolders.htm
UPDATE: You can also use Tweak UI to adjust user shell folders. This is useful in the case above, or if you want to make an adjustment such as keeping "My Documents" and the Desktop folder on the same drive. Within Tweak UI, the user shell folders setting is in My Computer-Special Folders.
