New Post: Error Provisioning Secure Store Service Application

I've had the same problem with my own deploymentscript.
This problem occures if you configure the secure store service application on a multi-server-sharepoint-farm.

I figured out, that the service instance "Secure Store Service" first starts on a diffent App-Server than the one you want to create the Keys for secure store.

Resolution:
You should implement a codesnipet before using the cmdlet 'Update-SPSecureStoreMasterKey' and 'Update-SPSecureStoreApplicationServerKey'.

Here is my Code I've used and it works pretty well:

Write-Host "Checking Secure Store Service Instance to be online..."
$SecStoreState = (Get-SPServiceInstance | ? {$_.TypeName -eq "Secure Store Service"} | ? {$_.Server.Name -eq $env:ComputerName}).Status
if ($SecStoreState -ne "Online") {
     Write-Host "Current state of secure store service application is: $SecStoreState ... trying to bring online now..."
     $SecStoreId = (Get-SPServiceInstance | ? {$_.TypeName -eq "Secure Store Service"} | ? {$_.Server.Name -eq $env:ComputerName}).Id.Guid
     Start-SPServiceInstance -Identity $SecStoreId
     while ($SecStoreState -ne "Online") {
          Write-Host "..." -NoNewLine
          $SecStoreState = (Get-SPServiceInstance | ? {$_.TypeName -eq "Secure Store Service"} | ? {$_.Server.Name -eq $env:ComputerName}).Status
     }
     Write-Host ""
}
Write-Host "Done."

Hope this will help you... it does for me.