Eric, no idea regarding the cause of your troubles. Have not run into them yet.
Regarding the system database, use usually use the target production environment for testing. That way we backup the System database and restore if needed after the final conversion. We haven't tried moving the 3 tables you refer to via scripting. It should work so long as you have ALL the files needed and connected. My concern would be specific to primary and foreign keys along with all referenced keys in other tables. Since I have not attempted to do this, I don't know where to point you to Eric. Just be careful and test well.