You can visit this topic on our support forum, my partner have been explain the permalink structure for portfolio right here : http://support.jegtheme.com/forums/topic/permalink-issue/
And this is first trick : Go edit your Portfolio List (Page with Portfolio template) then just click Update button without touching anything else (it will refresh permalink structure for portfolio).
It’s weird for me about your problem. As you know, we are not support for 3rd Party Plugins. If it caused by other plugin you need to contact the plugin author because that is out of our support territory.