A way to solve the problem of programs in the Startup folder being executed twice on Windows XP logon. The applications may appear doubled in msconfig.
Under Windows XP, programs placed in the Start Menu\Programs\Startup folder may be running twice. This occurs even though only one shortcut or icon for each program appears in the Startup folder when viewed through Windows Explorer. When you use msconfig (Startup tab) or autoruns (Logon tab) to inspect the Startup listings, they appear twice. Unchecking one or both disables the program from running at all.
This situation can occur if the user-specific Startup folder is deleted from the user's profile. When that happens, Windows looks for user-specific startup programs in the All Users startup folder instead. This causes doubling, because the programs from the All Users startup folder are executed once for All Users and again for the current user.
First, recreate the Start Menu folders in your profile directory, while logged in as the user experiencing the problem. Open Windows Explorer and browse to c:\Documents and Settings\USER\Start Menu. You can also type %USERPROFILE% in the address bar, and then open the Start Menu folder. Under the Start Menu folder, create a folder called Programs. Under Programs, create folders for Administrative Tools and Startup.
Now that the folders are recreated, you need to edit the registry so that Windows know where the user-specific Startup folder is located. Run regedit from the Start→Run... menu.
Open the following branch:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders
Under this branch, you may find some folders being listed under %ALLUSERSPROFILE%. These need to be changed to the %USERPROFILE% directory. Below you can see the resulting values of the keys that may need changing.
You do not need to edit the related values under the Explorer\Shell Folders branch, because the above settings will take precedence. You may want to check it anyway, just to be sure you didn't miss any folders, like Administrative Tools. After these changes are done, you may need to reboot to see the changes.
Run msconfig or autoruns and the doubled programs should be gone.
If you are uncomfortable editing the registry, you can use the Tweak UI Windows XP Power Toy. Run Tweak UI and then open the My Computer→Special Folders pane. Select the folders and set their paths as described above.
Some programs are supposed to have two Startup entries. This article only applies to Startup programs in your Start Menu, and when they are all doubled. This is probably a rare problem.