Yes, the registry entries are created, but into a different path, for instance:
HKEY_LOCAL_MACHINE\SYSTEM\ControlSet001\Control\Class{990a2bd7-e738-46c7-b26f-1cf8fb9f1391}\0000\SOFTWARE\Microsoft\Cryptography\Calais\SmartCards
Try to search your driver's name on registry editor starting from HKEY_LOCAL_MACHINE and you will find them.
When you use HKR, the path where registry entries are created changes, but you did not change the path you read from.
There is no choice, you have to touch driver source code.
I don't know still how, but here you are some clues:
Hope this helps.