I believe this is the case:
When you code javascript to execute "At run time" DE will trigger the javascript when the job is in Ready status, just prior to Exec status. When you resubmit a job it does not again go into ready status but goes straight to Exec.
You could put the javascript in an Alert and have that determine the submission count and who should be notified. I'm not sure that the Alert would execute prior to the email being sent, allowing you to set a variable to be used by the email. You could always use the Alert to choose the email and pass that to a separate application as a parameter, using that application to send the email.