Seriously? You got that working? I once wrecked my website trying to do that!
Right, so I’m wrong, your permalinks are somehow overwritten. I doubt by the theme, but do you use some kind of plugin for that portfolio? Does that plugin have some kind of settings?
I guess it’s time to start reading the themes files then. I’d start with the header.php, but that’s just a guess. I’m not much of a coder btw, so if it’s really your theme and it’s not really obvious, it’s most likely beyond me.