It's because up until very recently the BaseUrl setting was added to SiteSettingsPartRecord.
This was producing an upgrade error. So they changed it so a new table was created to hold the BaseUrl setting. But this was still in the same-numbered Update migration so if you already had the old BaseUrl setting you won't get the new update.
You could try fixing this by going to the "Orchard_Framework_DataMigrationRecord" table, find the entry for "Orchard.Core.Settings.Migrations", and subtract 1 from the Version number. This *should* cause the migration to be runnable again.
Let me know if it works.