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I have an office 365 SharePoint site. I have applied a custom master page using CSOM powershell on my root site and it is applied on the site but the Master page is not applying on site settings page. When I see in site settings -> master page, the value is set as my custom master page in both

  1. Site Master Page
  2. System master page

any idea?

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Try this script

 ##============================================ Setup Input Paths ===========================================================

 cls

 $Host.UI.RawUI.WindowTitle = "-- Change the Master Page to the Custom Master Page --"

 $StartDate = Get-Date
 Write-Host -ForegroundColor White "------------------------------------"
 Write-Host -ForegroundColor White "| Change the Master Page to the Custom Master Page |"
 Write-Host -ForegroundColor White "| Started on: $StartDate |"
 Write-Host -ForegroundColor White "------------------------------------"

 $LogTime = Get-Date -Format yyyy-MM-dd_hh-mm
 $LogFile = ".\ChangeMasterPage-$LogTime.rtf"

 #start-transcript $logfile

 $scriptBase = split-path $SCRIPT:MyInvocation.MyCommand.Path -parent
 Set-Location $scriptBase

 $ErrorActionPreference = "Stop"

 function AddPowerShellSnapin()
 {
     try
     {
         Write-Host "Adding PowerShell Snap-in" -ForegroundColor Green
         # Try to get the PowerShell Snappin.  If not, then adding the PowerShell snappin on the Catch Block
         Get-PSSnapin "Microsoft.SharePoint.PowerShell"
     }
     catch
     {
         if($Error[0].Exception.Message.Contains("No Windows PowerShell snap-ins matching the pattern 'Microsoft.SharePoint.PowerShell' were found"))
         {
             Add-PSSnapin "Microsoft.SharePoint.PowerShell"
         }
     }
     Write-Host "Finished Adding PowerShell Snap-in" -ForegroundColor Green
 }

 function UpdateMasterPage([string]$webURL)
 {
     $web = Get-SPWeb $webURL
 #Change the masterpage
     $web.CustomMasterUrl = "/services/GVI/_catalogs/masterpage/MyMaster.master"

 #Change the System Master Page
     $web.MasterUrl = "/services/GVI/_catalogs/masterpage/ MyMaster-System.master"
     $web.Update()
 }

 try
 {
     [void][System.Reflection.Assembly]::LoadWithPartialName("Microsoft.Sharepoint")
     [void][System.Reflection.Assembly]::LoadWithPartialName("Microsoft.Sharepoint.Administration")

     $ConfigXmlPath = $scriptBase + "\ConfigXML\Configuration.xml"
     Write-Host "Read the Config Values" -ForegroundColor Green 
     [Xml]$Config = Get-Content $ConfigXmlPath 

     AddPowerShellSnapin

     UpdateMasterPage $Config.Configuration.PublishingSite.URL  

 }
 catch
 {
     Write-Host "Custom Exception Happened on Main : " + $Error[0].Exception.Message -ForegroundColor Red  
 }

And the Config XML Will be like,

 <Configuration EnvironmentName="Dev/QA/UAT/PROD">
   <PublishingSite URL="http://MySiteCollectionURL" />

 </Configuration>

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