I haven't had this problem. I would check the file for damage by running Recover on the file.
In Manage | Layouts, you are not looking at table names. You are looking at table occurrence names. If you have a table occurrence (a "box" in manage | database | relationships) with exactly the same name, renaming it's data source table on the tables tab should automatically rename the matching table occurrence, but if you have changed the name of the table occurrence or created new table occurrences, then these occurrences will not update to a different name when you rename a table over on the tables tab.