With the new version of Provisioning Server Citrix changed the management console ports from 8000 and 8001 to 54321 and 54322. The reason for this change is so that PVS can be installed on the XenDesktop Desktop Delivery Controller without port conflicts.
The port change breaks the the XenDesktop Setup Wizard because by default the setup wizard tries to communicate with PVS on ports 8000 and 8001.
To fix this you must edit the SetupToolApplication.exe.config file that is located in the “C:\Program Files\Citrix\XenDesktop Setup Wizard” folder and change the two ports from 8000 to 54321 and from 8001 to 54322.
The Provisioning Server 5.1 release notes states that you only have to change the 8000 port but in my experience I had to change both.