Hi John and welcome to Digi Forum.
The behavior you describe is expected, the port isolated / hub mode is not a config setting so is not automatically imported.
If you want to avoid to do it manually, a way is to edit the config.da0 file with a text editor, adding the Port Isolated command "ethvlan" at the end. Then, you would need to reboot the device twice. After the second reboot, the command will be applied and the router will be in port isolated mode.
I hope this helps, for any further assistance, please review our support options on our website: https://www.digi.com/support
Digi Technical Support Team