When you alter your startup with MSCONFIG.EXE, you are prompted at the next start up with a System Configuration Utility window that explains that You have used the System Configuration Utility....
You can check the Don't show this message or launch the System Configuration Utility when Windows starts box to prevent future warnings, or you can:
1. When the System Confuration Utility window prompts you to restart, choose Exit Without Restart.
2. Use the Registry Editor to navigate to HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run\MSConfig and delete the MSConfig key.
3. If desired, restart your computer.
NOTE: You can also run regedit /s <PATH>\MSConfig.reg, by using the technique from tip 4012, where <PATH>\MSConfig.reg contains:
REGEDIT4 \[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run\] "MSConfig"=-