Make sure you set your completion settings up first before turning 'Email students' to 'On' otherwise when the cron runs it will email them as you have made it accessible to all those enrolled in the course. Also, make note the certificate and custom certificate plugins are completely separate and there is no cross-over whatsoever. Getting an issued certificate in one does not mean that it is also issued in another.
Custom certificate (plugin)
Custom Certificate emailing all students
This discussion has been locked so you can no longer reply to it.