Using $site | Set-Item does not save changes back to IIS site

I'm in the process of writing some automated scripts to create/update IIS sites on a server using PowerShell.

The aim is to have a configuration object that can then be handled by a single script to do all the heavy lifting.

My config HashTable looks like this:

$config = @{
    AppPools = (
        @{
            Name="AppPool1"
            Properties = @{
                Enable32BitAppOnWin64=$true
                ManagedRuntimeVersion="v4.0"
                ProcessModel = @{
                    IdentityType = "NetworkService"
                }
            }
        }
    )
    Websites = (
        @{
            Name="Site1"
            Properties = @{
                PhysicalPath = "C:\sites\site1"
                ApplicationPool = "AppPool1"
            }
        }
    )    
}

My script then uses the config to process each application pool and web site:

 Import-Module WebAdministration

 $config.AppPools | 
    % {
        $poolPath = "IIS:\AppPools\$($_.Name)"
        
        # Create if not exists
        if(-not(Test-Path $poolPath)){ New-WebAppPool $_.Name }            
        
        # Update the properties from the config
        $pool = Get-Item $poolPath
        Set-PropertiesFromHash $pool $_.Properties
        $pool | Set-Item            
    }
        
 $config.Websites | 
    %{        
        $sitePath = "IIS:\Sites\$($_.Name)"
            
        # Create if not exists
        if(-not(Test-Path $sitePath)){ New-WebSite $_.Name -HostHeader $_.Name }
            
        # Update the properties from the config
        $site = Get-Item $sitePath
        Set-PropertiesFromHash $site $_.Properties
        $site | Set-Item 
    }      

As you can see the process is virtually identical (apart from the item paths and type being created). This will of course be refactored if I get