there has been an updated release of the silverlight tools for visual studio beta 2. it's being pushed to the download servers now, so propogation might take some time.
this update resolves some issues people have been reporting about broken references and certain anomalies with visual studio 2008. you should uninstall the old silverlight tools release before installing to ensure you get the updates. there is no need to uninstall the silverlight alpha refresh runtime.
get the update here: updated silverlight tools for visual studio.