We're using the latest version of Portfolio with JIRA and I've run the wizard and imported the Epics and Stories from our JIRA instance, but I can't allocate themes now to stories and/or Epics in Portfolio and there doesn't appear to be any way of doing this in JIRA itself.
I've got the Scope view open in Portfolio, but the column under Theme is not clickable, so dropdown of the themes I have set up is visible. As you can see from the screenshot, the area gets a blue border but no dropdown.