I found that using ICACLS does the job, but when you look at the permissions on the folder, they are all listed as "Special Permissions". Functionally sufficient, but somewhat annoying if you have Help desk folks just checking to see if someone has rights.
I found that using the cmdlets in PowerShell actually listed the rights properly after execution. Figure I'd include what I found, and what I'm using. This is assuming you're creating the User's folder directly at the \\server\share path.
$acl = Get-Acl \\SERVER\SHARE\%username%
$acl.SetAccessRuleProtection($True, $False)
$rule = New-Object System.Security.AccessControl.FileSystemAccessRule(“ADMINISTRATORS”,”FullControl”, “ContainerInherit, ObjectInherit”, “None”, “Allow”)
$acl.AddAccessRule($rule)
$rule = New-Object System.Security.AccessControl.FileSystemAccessRule(“HELPDESK”,”FullControl”, “ContainerInherit, ObjectInherit”, “None”, “Allow”)
$acl.AddAccessRule($rule)
$rule = New-Object System.Security.AccessControl.FileSystemAccessRule("DOMAIN\%username%",”Read,Write,Delete,Modify”, “ContainerInherit, ObjectInherit”, “None”, “Allow”)
$acl.AddAccessRule($rule)
Set-Acl \\SERVER\SHARE\%username% $acl