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Cleanup old msconfig entries

MSCONFIG (System Configuration Utility) is a frequently used utility to manage the startup applications. This utility, however does not have an option to delete the entries. The entry which you've unchecked a long time back may still show up, while the application may have been uninstalled already.

To remove the invalid entries in MSCONFIG, you need to edit the registry or use a third-party utility.

Locations of the entries in MSConfig
The enabled/checked items might be present in any of these locations in the registry:
[HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Run]

[HKCU\SOFTWARE\Microsoft\Windows\CurrentVersion\Run]

 [HKCU\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Windows]

In the right-pane, the values named Run & Load
The disabled entries are present in any of the locations:
[HKLM\SOFTWARE\Microsoft\Shared Tools\MSConfig\startupreg]

[HKLM\SOFTWARE\Microsoft\Shared Tools\MSConfig\startupfolder]

To remove the entries, open Regedit.exe and navigate to the above paths.
Backup the registry key before deleting it.
Disabled items are stored as a per-machine basis (HKLM?).
The hkey string value stores the location where the entry was originally and when the user re-checks the entry, the hkey value determines whether to place the entry back to HKCU or HKLM

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