Symptoms
Assume that you have the Microsoft PowerShell ExecutionPolicy of the SMART hardware ships set to Bypass, and you try to update the SMART system from Microsoft Skype for Business 2015 (Lync 2013) to Microsoft Skype for Business 2016. When you try to run the SetAppLockerPolicy.ps1 PowerShell script, the update hangs in the ConfigureSystem step. This issue occurs because while the script is signed, the signing certificate isn't found in the "Trusted Publishers" devices in the certificate store.
Resolution
To fix this issue, install the January 3, 2017, update (KB3128049) for Skype for Business 2016.