Best thing to reduce the chances of problems with PST's going into the wrong mailbox is to mark them. Go to the Advanced properties of the mailbox policy and under Desktop settings set "Mark PST Files" to On. However, this only works when the pst's are currently being accessed by the actual owner. If this isn't true then marking won't work.
If your mailboxes are running out of quota your only three options are:
1) Don't make shortcuts in the mailbox. Keep in mind the shortcuts are only a convenience for the users, they can still get to archived mail via search.asp or Archive Explorer.
2) Up the quota.
3) Reduce some of the other mail in the mailboxes. Set your policy to archive by quota and leave more space in the mailbox. Then run archiving BEFORE you run PST migration to ensure there's plenty of room.
Those are some thoughts. If you're having any other specific issues please post.
