Google Apps Sync for Microsoft Outlook
I had this happen. Because I used Google Apps Sync for Outlook to perform the migration instead of using the Outlook Migration tool.
I'm guessing you probably did the same. Contrary to what some believe GASMO is a horrible migration tool, it was never designed for that.
Here's how I fixed it.
Take Outlook offline.
Open the datafile that contains the email history * Copy* the new emails from the current datafile to the datafile with the email history. I do this because I had tons of folders under the inbox and needed to preserve that labeling structure and make sure I migrated all the emails.
Close outlook and run the Outlook migration tool on the datafile with the entire email history. Don't worry about duplicates as the message ID are used to determine dupes.
When its done log into Outlook, take it offline, and detach the history datafile.
All the history should start syncing down from the mail servers when you bring Outlook online.