Client migration doesnt use the markings as the mailbox is determined by the connecting client.
The Outlook add on will search for all PST's on the local disks and migrate them unless you use the policy setting limiting them to the client user's Document and Settings folder and subfolders.
So what is happening is normal behavior. I know there has been talk in the past about changing that to allow more granular folder selection or limitations but that is not currently on the roadmap.
I know there is a good whitepaper on it as well, but I found this one article specific for Client Side Migration written by one of the Backline Engineers.
https://www-secure.symantec.com/connect/articles/client-side-migration-process