We can give you some code to disable the emails in JFBConnect if you'd like. To disable the system notifications for each user, you'd need to either edit them in the User Manager in the admin area and set "Receive System Emails" to "No" for any users that you don't want to receive them or run a SQL query on your server to set all users to 'No'... then, you can use the User Manager to re-enable it for the admin(s) you really want to receive those mails.
Hope that helps, but if you need more instructions on the code changes or other assistance, just let us know. We wouldn't recommend the code change as you'll have to do it after every upgrade and it will also disable the email going to you (the admin). We'd highly recommend disabling the "Receive System Emails" for the user's that shouldn't be getting them.
Do you know why that setting is enabled for users? I'm still assuming that it is the problem, but if it's not enabled for users, let us know as it may be some other issue.
Thanks,
Alex