Is the message alert coming from Windows Defender or MsConfig? When you alter something in MSConfig you are prompted at the next start up with a System Configuration Utility window that explains that you have used the System Configuration Utility. Check the "
Don't show this message or launch the System Configuration Utility when Windows starts" box to prevent future warnings from appearing.
MSConfig is a
troubleshooting utility used to diagnose and fix system configuration issues. In the
Summary section Microsoft says "
The System Configuration utility helps you find problems with your Windows XP configuration. It does not manage the programs that run when Windows starts."
Although it works as a basic startup manager,
msconfig should not be used routinely to disable auto-start programs. It is a temporary solution and not a good practice for the following reasons:
- When uninstalling programs while disabled with msconfig, they may not be uninstalled properly and manually editing the registry will be required to remove everything.
- Msconfig will often leave orphaned entries when software is uninstalled. When used to switch back to normal startup mode, these orphan entries can result in boot up errors.
- Msconfig allows malware related items to hide in your registry which you may not see or affect your computer until switched back to normal startup mode. This could then result in reinfection of the computer.
- Msconfig does not list all applications loaded in all possible startup locations (some entry points are hidden and unknown to the user) and does not allow the complete removal of disabled entries from its list.
You should not use msconfig to disable startup applications related to a running service. Doing so alters the registry and there are services that are essential for hardware and booting your system. When you uncheck a service in msconfig, you completely disable it.
If you uncheck the wrong one, you may not be able to restart your computer. You should only disable services using Control Panel > Administrative Tools > Services.
A better alternative is to use a
startup manager like
Startup Control Panel,
Autoruns, or
Starter by CodeStuff.