You may find that some things will work in the Lync GUI that will not work in PowerShell (Access Denied), the reason for this is that RBAC only applies to remote PowerShell and local PowerShell uses the AD permissions and not RBAC.
To resolve this you can login to PowerShell using the following script: (Copy the contents to a file and name it Connect-Lync.ps1)
$usercredential = get-credential
$pso = new-pssessionoption -skipcacheck -SkipCNCheck -SkipRevocationCheck
$session= New-PSSession -ConnectionUri https://localhost/ocspowershell -credential $usercredential -sessionoption $pso
Note: 1. This script ignores the certificate (so it will work if your using a self signed cert)
2. You may need to modify the execution policy to run this unsigned script in PowerShell “set-executionpolicy remote”
“Note that RBAC applies only to remote management. If you are logged on to a computer running Lync Server 2010 and you open Lync Server Management Shell, RBAC roles will not be enforced. Instead, security is enforced primarily through the security groups RTCUniversalServerAdmins; RTCUniversalUserAdmins; and RTCUniversalReadOnlyAdmins.”