Starting with version 8.1 there is a specific event to set the port number of the Job Server.
In Object Browser navigate to QBMServer | Select the Job Server | Expand Events from Actions window | Click SetPort | Enter the port number | Click Generate. E.g.:
This will generate the QBMServer update process to update the port number in the database. Once the process is finished, start/restart the job service. This should generate another event, GETCONFIG. Once finished, the job server should pick up the updated port number.