Your sender MTA sends multiple email messages over one SMTP connection. But, it sends them without closing the connection to the ATD/IS Email Connector between each send.
The Email Connector calculates the ATD/IS scan timeout by comparing the delta between the current time and the SMTP connection establishment time. It doesn't use the delta between the current time and arrival time of an individual email message.
The sender MTA reuses an SMTP connection without sending the
QUIT command. The time spent sending the previous email messages as part of this connection is added to the timeout timer.
This time eventually exceeds your scan timeout setting value.