Cannot Delete/Remove Startup Programs in MSCONFIG for WinXP Pro

I have a Toshiba Laptop with Windows XP professional. My problem is when I unchecked some startup entries in MSCONFIG and then restart my computer, the startup entries reappears again. I mean there would be a double startup entry (one is check and the other is uncheck for the same startup entry). How do I permanently delete the startup entries in the msconfig. I also used msconfig cleanup utility but it didn't work. I don't have any spyware or virus in my computer. Thanks for the help.