When migrating to SP5GA the latest version of DBAdminTool must be used. The version shipped with SP5GA contains a bug when generating ids for exposed stories and sections in templates during import. The generated ids will in some cases not correspond to the ids generated by StoryTeller, which will cause sections and exposed stories with mismatching ids to be removed from document definitions during template synchronization as they appear to not exist anymore.
This applies to everyone migrating a project containing StoryTeller processes to SP5GA!
The latest version can be found here: http://streamshare.streamserve.com/Downloads/?navid=53296
StreamServe Technical Support