Finally! This problem was bugging me for so long – I just now thought to research it and found this article. Very helpful!
Prevent Startup Programs from Running Twice in Windows XP
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 MenuProgramsStartup 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.