Tim, it would be impossible for me to diagnose what yoy may be experiencing with this information. I will need, at the veryleast, your PKG file so that I can deploy it here and see if it is reproducable. If so, then I will be able to debug this and try and determine what you are running into.Also, we are about to post a new beta that has full SQL Server 2008 support for the DDT as well as all other areas of the framework. In the process of updating this, we moved to SMO 10 which required that we make a few modifications to the migrator class.
Finally, the environment to which you are deploying can also make a difference. If there is something with a pre-deployed database that is unexpected by SMO and the migrator class, then this could be a factor as well. So let's start with a PKG file and go from there.