I believe the only solution is to train the technicians to send emails from their own account and carbon copy the Track-It! account and NOT use the shared email account Track-It! uses to send emails manually. This rule is in place so that rules don't go off the rails and create an endless stream of emails. Imagine if an email sent from the Track-It! account to the Track-It! account sent back an auto response, to itself, and then based on teh rules, that auto response was read and generated another auto response. Or worse, if the rules were configured to treat every email as a new ticket, then the looping emails would generate thousands of tickets in a very short time. This is set up to NOT allow the Track-It! email box to email itself for these reasons.
I would agree with Cris. Track-It! is designed to work with its own "system" email account... not one shared by multiple people.
I would recommend that you consider removing the technicians' rights to that shared mailbox. This would ensure the correct human behavior. The end result would be one where any email to clients would either be sent from within Track-It! (automatically recording the interaction in the ticket) or by technicians using the method Cris described where they send it from their personal account.