Indeed SSRS 2008 does not rely anymore on IIS. That should not prevent configuration however. One thing I’m not sure, had you already run the server configuration tool when you receive the error you mentioned in your first post?
If not, are you still receiving the error after configuration?
If yes, could you try the following :
Run Reporting Services configuration manager
Stop the report server.
Start the report server again.
Let me know.
Regards,