If I remember correctly you should install the preparation files for SU/RU upgrade from CLI on CUCM as they are not supposed to be installed with PCD. The reason for this is because it will restart the PAWS service that PCD relies on for communication to CUCM. Once the preparation files are installed you should be able to run the rest of the steps from PCD.
If you have read the upgrade guide you would know that. RU means Refresh Upgrade and SU means Service Upgrade.
