The new version of the Visual Studio 2008 extensions for SharePoint 1.3 include some changes to support install on x64 OS. Specifically it creates a WCF web service that is required to run in x64 and communication with x64 SharePoint. The x86 Visual Studio 2008 makes calls to this web service to do certain SharePoint operations.
The web service is secured so it can only be called by Visual Studio 2008 running on the same machine. We also do not automatically give the web service the required permissions to make calls into SharePoint. The installer notes this, but it's easy to overlook, that you have to add these permissions.
Steve Fox just wrote up a great screen shotted guide for how to do this for Windows Server 2008 here.