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
import-pssession $session
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”
References: