I am setting up your template. I have entered in a bunch of portfolio projects and have a few categories. When I go to create a menu for the portfolio section, I only have my BLOG/Post categories to choose from.
If this helps, here is the temp URL: http://18.104.22.168/~techcar2/portfolio and you see that the category websites is from my FAQs/Articles section. My portfolio categories should be CMS, WordPress, Custom, All, etc. Those are not taxonomies that are available when I go to create a menu. Any thoughts? I hope I am being clear enough....I can insert a photo of the menus area if that helps.