Msconfig.exe's dialog re-appears 
Msconfig.exe runs on reboot by inserting an entry named MSConfig under the registry key HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run. To prevent the dialog box from showing up, you can manually delete the MSConfig entry, use the Console Registry Tool (reg.exe) to delete it, or use a batch file to delete it.

reg delete HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Run /v msconfig /f

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