I've got this working now
and I left the keys where they were in HKEY_LOCAL_MACHINE\Software\Research In Motion\BlackBerry Enterprise Server\Database
The problem was with the LocalSystem account that Lotus Domino Server service starts with.
See this KB article KB-03543 at the BlackBerry Technical Knowledge Center
Only problem is that you can't have the service interact with the desktop when you change the account that the service starts with so you don't get a console when the server starts. I've got around this by using a Java Console.
Add -jc to the end of the cmd line for the service, you have to do this via registry
HKEY_LOCAL_MACHINE\SYSTEM\ControlSet001\Services\L otus Domino Server (LotusDominoData)
Add -jc to the end of the ImagePath value
You then run the jconsole.exe to see it
Hope this helps anyone.