Finally both versions of SilverlightDesktop have been upgraded to Silverlight 3.0 The most important thing was that you no longer have to edit the web.config to install it in DNN4 :)
We also had to fix a bug with DNN5. We were passing the DNN Core UserInfo object to the WhoAmI module but it appears additional properties were added to this class that would not serialize so the module broke.
It was an easy fix to make our own custom object and use that to pass user information to the Silverlight WhoAmI module.