That's not an issue we've seen or heard of before. We don't perform any direct edits to the menu table in Joomla, so I'm not even sure how that error would be occurring.
Can you tell me what version of JFBConnect you're upgrading from? Also, are you using a MySQL database or Postgres?
Beyond that, the installation process does disable all plugins before it starts. That prevents some common problems. Since the installation didn't perform normally, they wouldn't have been re-enabled as they should have been. However, your sourcecoast.css overrides in your template directory should not have been modified at all. That's bizarre.
If you have any other details on your setup, update process or details that you can help provide to us, that would really help.
Thanks,
Alex