There's currently a limitation with the restore tool that ships with MOSS2007 and WSSv3. If you're trying to restore multiple web applications that are hosted on the same port using host headers, the restore will only restore one of the web applications. To get around this, you must restore each web application one at a time. After the web application has been restored, you will need to update the host header information in IIS, the alternate accessing mapping in SharePoint and proceed to restore the next web application.