I'm not sure why you're seeing that error message. Can you do the following:
1) In the Autotune -> Facebook Application area, hit the "Refresh" button in the top right
2) Click "Save Custom Settings". That shouldn't change any of your settings, but will try to re-save the migrations
If that still doesn't work, can you let me know what migrations are listed in the "Migrations" tab?
Thanks,
Alex