When deploying Windows Server 2012 R2 in VirtualBox using Microsoft's official .vhd image, many administrators encounter this critical Server Manager startup failure:

Server Manager cannot run because of an error in a user settings file. 
The configuration section 'connectionStrings' has an unexpected declaration.

This typically occurs after performing common post-installation tasks like:

• Computer name changes
• Execution policy modifications
• Initial configuration steps

The CLR20r3 error (Problem Signature 01: servermanager.exe) indicates a .NET runtime issue in the Server Manager application. The key components involved are:

System.Configuration (4.0.30319.33440)
Windows Server Manager (6.3.9600.16384)

The error suggests corruption in either:

1. The Server Manager's configuration files
2. Underlying .NET Framework components
3. WMI namespace configurations

While standard troubleshooting steps (Windows Updates, DISM repairs) often fail, these advanced methods have proven effective:

1. Complete Configuration Reset

Delete all Server Manager configuration files and let them regenerate:

# PowerShell command to purge Server Manager settings
Stop-Process -Name ServerManager -Force
Remove-Item -Path "$env:APPDATA\\Microsoft\\Windows\\ServerManager\\*" -Recurse -Force

2. Manual Registry Repair

Fix potential WMI namespace issues referenced in the WMIDiag output:

# Registry patch to reset WMI namespaces
reg add "HKLM\\SOFTWARE\\Microsoft\\WBEM" /v "Installation Directory" /t REG_SZ /d "%windir%\\system32\\wbem" /f
reg add "HKLM\\SOFTWARE\\Microsoft\\WBEM" /v "Repository Directory" /t REG_SZ /d "%windir%\\system32\\wbem\\repository" /f

3. .NET Framework Configuration Reset

Recreate the machine.config file that Server Manager depends on:

# Reset .NET configuration
%windir%\\Microsoft.NET\\Framework64\\v4.0.30319\\aspnet_regiis.exe -i

To avoid this issue when setting up new Windows Server 2012 R2 instances:

1. Complete all Windows Updates before renaming the computer
2. Run this PowerShell script to prepare Server Manager:

# Pre-configuration script
if (-not (Test-Path "$env:APPDATA\\Microsoft\\Windows\\ServerManager")) {
    New-Item -Path "$env:APPDATA\\Microsoft\\Windows\\ServerManager" -ItemType Directory
}
Set-Content -Path "$env:APPDATA\\Microsoft\\Windows\\ServerManager\\ServerList.xml" -Value "<Servers></Servers>"

If the error persists after trying all solutions:

• Export your server roles/configurations using:

Export-WindowsDriver -Online -Destination D:\\Drivers
Export-SmigServerSetting -featureID -path C:\\config.sms

Then redeploy using the original .vhd and import your configurations.

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After deploying Windows Server 2012 R2 via a Microsoft-provided VHD in VirtualBox, many administrators encounter this specific Server Manager failure when renaming the host computer. The core error manifests in two phases:

// Phase 1 Error
Server Manager cannot run because of an error in a user settings file.
The configuration section 'connectionStrings' has an unexpected declaration.

// Phase 2 Crash
Problem Event Name: CLR20r3
Fault Module: System.Configuration (4.0.30319.33440)

The issue stems from configuration file corruption during computer rename operations. Server Manager maintains multiple configuration stores:

• Registry: HKLM\SOFTWARE\Microsoft\ServerManager
• File: C:\Users\[User]\AppData\Roaming\Microsoft\Windows\ServerManager\ServerList.xml
• .NET config: C:\Windows\System32\ServerManager.exe.config

The CLR20r3 error indicates the .NET runtime encountered an unhandled exception while parsing these configurations.

1. Configuration Reset Method

First try resetting all Server Manager configurations:

# PowerShell Admin Console
Stop-Process -Name ServerManager -Force
Remove-Item -Path "$env:APPDATA\Microsoft\Windows\ServerManager\*" -Recurse -Force
Remove-ItemProperty -Path "HKLM:\SOFTWARE\Microsoft\ServerManager" -Name "DoNotOpenServerManagerAtLogon" -ErrorAction SilentlyContinue
Get-AppxPackage -Name *servermanager* | Reset-AppxPackage
Start-Service -Name SessionEnv

2. .NET Framework Repair

Since System.Configuration is failing, repair .NET 4.5/4.6:

dism /online /cleanup-image /restorehealth
sfc /scannow
"$env:SystemRoot\Microsoft.NET\Framework64\v4.0.30319\SetupCache\Setup.exe" /repair /x86 /x64 /ia64 /norestart

3. WMI Namespace Repair

The WMIDiag error suggests WMI corruption:

winmgmt /verifyrepository  # Check consistency
winmgmt /salvagerepository # Attempt repair
winmgmt /resetrepository   # Nuclear option

For persistent cases, directly modify the ServerManager registry:

Windows Registry Editor Version 5.00

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\ServerManager]
"DoNotOpenServerManagerAtLogon"=dword:00000000

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\ServerManager\Oobe]
"PostOobeAction"=dword:00000000

When working with VHD-based deployments:

1. Complete Windows Update before any configuration changes
2. Create registry backups before renaming computers:

   reg export HKLM\SOFTWARE\Microsoft\ServerManager C:\sm_regbackup.reg

3. Use sysprep before capturing golden images