MSConfig is a really handy utility. I use it all the time to remove items from the system’s startup that I may want to add again later. (Printer utilities, sound drivers, etc) However, there are often plenty of items that you may wish to permanently remove from MSConfig startup area.
To get rid of the extra entries you must edit the registry.
Start regedit (Start->Run and type REGEDIT, then press OK).
Browse to HKLM*SOFTWAREMicrosoftShared ToolsMSConfigstartupreg
and HKLMSOFTWAREMicrosoftShared ToolsMSConfigstartupfolder
Delete any items listed in there that you no longer want shown unchecked in MSConfig
*HKLM refers to HKEY_LOCAL_MACHINE