Registry script is changing 5 of 6 keys

Anton_Howard I did some testing and wrote a slightly changed version of your script:

#Set keys
$CertPaddingCheckPaths = @("HKLM:\Software\Microsoft\Cryptography\Wintrust\Config", "HKLM:\Software\Wow6432Node\Microsoft\Cryptography\Wintrust\Config")
$SecuritySignaturePaths = @("HKLM:\System\CurrentControlSet\Services\LanManWorkstation\Parameters", "HKLM:\System\CurrentControlSet\Services\LanManServer\Parameters")
$EnableCertPaddingCheckKey = "EnableCertPaddingCheck"
$RequireSecuritySignatureKey = "RequireSecuritySignature"
$KeyValue = "1"

#CertPadding
foreach ($CertPaddingCheckPath in $CertPaddingCheckPaths) {
    # Create the registry key if it doesn't exist
    if (!(Test-Path $CertPaddingCheckPath)) {
        New-Item -Path $CertPaddingCheckPath -Force -ItemType Directory | Out-Null
        Write-Host Created $CertPaddingCheckPath
    }
    # Create or update the registry value
    Set-ItemProperty -Path $CertPaddingCheckPath -Name $EnableCertPaddingCheckKey -Value $KeyValue -Type DWORD
}

#SecuritySignature
foreach ($SecuritySignaturePath in $SecuritySignaturePaths) {
    # Create the registry key if it doesn't exist
    if (!(Test-Path $SecuritySignaturePath)) {
        New-Item -Path $SecuritySignaturePath -Force -ItemType Directory | Out-Null
        Write-Host Created $SecuritySignaturePath
    }
    # Create or update the registry value
    Set-ItemProperty -Path $SecuritySignaturePath -Name $RequireSecuritySignatureKey -Value $KeyValue -Type DWORD
}

Write-Host "Registry keys and values have been created or updated successfully."

But the same issue, HKLM:\Software\Microsoft\Cryptography\Wintrust\Config doesn't get created... So I enabled some Transcript logging (Start-Transcript), and if I just do a new-item