Hey Carla,
That is strange... Those tables should be filled with migrated ids. You see, when you migrate some post from WordPress, post id with new Joomla id and parent id are written into cmigrator_articles table. Same thing is happening with other tables except cmigrator_configuration which stores configuration data you entered on making new configuration for migration. So, in your case, it seem only users are migrated? Maybe you used user migration only after regular migration? On every migration, those tables are getting empty and fill with new data for new migration. If you are still having problems, you should make a new ticket in our ticket system where you can provide us with your database so we can take a look and find the problem.
Best Regards,
Petar