Run a system file checker

The first thing you will have to do in this case is to run a system file checker. First you will need to run an SFC scan to check for any errors and if there are you will have to proceed with the DISM command.

• Click Start, type Command Prompt or cmd in the Search box, right-click Command Prompt, and then click Run as administrator. If you are prompted for an administrator password or confirmation, type the password, or click Allow.
• First run the inbox Deployment Image Servicing and Management (DISM) tool prior to running the System File Checker
• Type the following command, and then press Enter.  It may take several minutes for the command operation to be completed. DISM.exe /Online /Cleanup-image /Restorehealth
• At the command prompt, type the following command, and then press ENTER:  sfc /scannow
• The sfc /scannow command will scan all protected system files, and replace corrupted files with a cached copy that is located in a compressed folder at %WinDir%\System32\dllcache.
• Do not close this Command Prompt window until the verification is 100% complete. The scan results will be shown after this process is finished.

You will be getting any of the following messages after the scan has been completed.

• Windows Resource Protection did not find any integrity violations: This means that you do not have any missing or corrupted system files.
• Windows Resource Protection could not perform the requested operation: To resolve this problem, perform the System File Checker scan in safe mode, and make sure that the PendingDeletes and PendingRenames folders exist under %WinDir%\WinSxS\Temp.
• Windows Resource Protection found corrupt files and successfully repaired them. Details are included in the CBS.Log %WinDir%\Logs\CBS\CBS.log.
• Windows Resource Protection found corrupt files but was unable to fix some of them. Details are included in the CBS.Log %WinDir%\Logs\CBS\CBS.log.

If you get the last message then you will need to repair the corrupted files manually by following the steps listed below.

• Open an elevated command prompt
• Type the following command, and then press ENTER: findstr /c:”[SR]” %windir%\Logs\CBS\CBS.log >”%userprofile%\Desktop\sfcdetails.txt”
• Open the Sfcdetails.txt file from your desktop.

When you find which system file was corrupted and could not be repaired through the detailed information in the Sfcdetails.txt file, find where the corrupted file is located, and then manually replace the corrupted file with a known good copy of the file. To do this, follow these steps:

• Take administrative ownership of the corrupted system file. To do this, at an elevated command prompt, copy and then paste (or type) the following command, and then press ENTER: takeown /f Path_And_File_Name
• The Path_And_File_Name placeholder represents the path and the file name of the corrupted file. For example, type takeown /f C:\windows\system32\jscript.dll.
• Grant administrators full access to the corrupted system file. To do this, copy and paste (or type) the following command, and then press ENTER: icacls Path_And_File_Name /GRANT ADMINISTRATORS:F
• Take note that the Path_And_File_Name placeholder represents the path and the file name of the corrupted file. For example, type icacls C:\windows\system32\jscript.dll /grant administrators:F.
• Replace the corrupted system file with a known good copy of the file. To do this, copy and paste (or type) the following command, and then press ENTER: Copy Source_File Destination
• Take note that the Source_File placeholder represents the path and file name of the known good copy of the file on your computer, and the Destination placeholder represents the path and file name of the corrupted file. For example, type copy E:\temp\jscript.dll C:\windows\system32\jscript.dll.

Check if the configuration system failed to initialize error still occurs.

Check the configuration files

There are times when the configuration files of the Microsoft .NET framework can cause this problem.

• Go to the following file path: C:\Windows\Microsoft.NET\Framework64\v2.0.50727\CONFIG
• Right-click on config file of the application of which the error occurs and select Edit (You can use Notepad++ for a clearer view of the config file instead of using the default notepad).
• Inside the config file, make sure that the first child under the title <configurations> is “configSections”. If you are getting an error, it may be possible that this isn’t the case. If it is, remove the configuration element present between the parent title “configurations” and the child title “configSections”.
• Restart your computer.

Check if the configuration system failed to initialize error still occurs.

Delete the configuration file of the application

If the problem is caused by the config file of a certain application then you should try to delete this file. It will be recreated once the application is opened again.

• Go to the following file paths: C:\Users\<Your Username>\AppData\Local and C:\Users\<Your Username>\AppData\Roaming
• Delete the application config file. You can delete or move the entire folder to a new location and rename it (in case you want to replace it back).
• Restart your computer.

Check if the configuration system failed to initialize error still occurs.

Perform a clean boot

When you do a clean boot you can pinpoint the third party application that could be causing this problem.

• Press Windows + R to launch the Run application.
• Type “msconfig” in the dialogue box and press Enter.
• Navigate to the Services tab present at the top of the screen. Check the line which says “Hide all Microsoft services”. Once you click this, all Microsoft related services will be disabled leaving behind all the third-party services.
• Click the “Disable all” button present at the near bottom at the left side of the window. All the third-party services will now be disabled.
• Click Apply to save changes and exit.
• Navigate to the Startup tab and click the option of “Open Task Manager”. You will be redirected to the task manager where all the applications/services which run when your computer starts will be listed.
• Select each service one by one and click “Disable” at the bottom right side of the window.
• Restart your computer.

Check if the configuration system failed to initialize error still occurs. If it doesn’t then there is an external program which was causing the problem. Search through your installed programs and determine which application is causing your problems.