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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.
Hmm, actually try going into Scope view and click the gear icon in the vertical middle of page on the right side, it will display a list of columns you can add. Look for one named Themes and click it. If it's not there, can you add a screenshot of what you have in that list?
Epic/Theme, which you have in your first screenshot, is a completely different column.
More than likely it's a custom field that was added to the plan. If you go into the plan configuration, via the three dot button next to the plan name and selecting Configure, then clicking Custom fields on the left side you'll see that there along with a few others according to your first screenshot.
Click on the Reports view to the right of Scope. The default should be the Themes report, but if not, click Switch Report and select Themes from that dropdown. You can add the Themes you want here, then they will be available in the Scope view.